{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T18:38:18Z","timestamp":1791398298600,"version":"4.3.3"},"publisher-location":"Cham","reference-count":342,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783319073941","type":"print"},{"value":"9783319073958","type":"electronic"}],"license":[{"start":{"date-parts":[[2014,1,1]],"date-time":"2014-01-01T00:00:00Z","timestamp":1388534400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014]]},"DOI":"10.1007\/82_2014_371","type":"book-chapter","created":{"date-parts":[[2014,5,15]],"date-time":"2014-05-15T04:34:38Z","timestamp":1400128478000},"page":"279-326","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Helper T Cell Plasticity: Impact of Extrinsic and Intrinsic Signals on Transcriptomes and Epigenomes"],"prefix":"10.1007","author":[{"given":"Michael","family":"Bonelli","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han-Yu","family":"Shih","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiyoshi","family":"Hirahara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kentner","family":"Singelton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arian","family":"Laurence","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda","family":"Poholek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"Hand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yohei","family":"Mikami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Golnaz","family":"Vahedi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuka","family":"Kanno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John J.","family":"O\u2019Shea","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,5,16]]},"reference":[{"issue":"10","key":"371_CR1","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1038\/ni1379","volume":"7","author":"I Abarrategui","year":"2006","unstructured":"Abarrategui I, Krangel MS (2006) Regulation of T cell receptor-alpha gene recombination by transcription. Nat Immunol 7(10):1109\u20131115. doi:10.1038\/ni1379","journal-title":"Nat Immunol"},{"issue":"20","key":"371_CR2","doi-asserted-by":"publisher","first-page":"4380","DOI":"10.1038\/sj.emboj.7601866","volume":"26","author":"I Abarrategui","year":"2007","unstructured":"Abarrategui I, Krangel MS (2007) Noncoding transcription controls downstream promoters to regulate T-cell receptor alpha recombination. EMBO J 26(20):4380\u20134390. doi:10.1038\/sj.emboj.7601866","journal-title":"EMBO J"},{"issue":"4","key":"371_CR3","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1038\/ni.2554","volume":"14","author":"AK Abbas","year":"2013","unstructured":"Abbas AK, Benoist C, Bluestone JA, Campbell DJ, Ghosh S, Hori S, Jiang S, Kuchroo VK, Mathis D, Roncarolo MG, Rudensky A, Sakaguchi S, Shevach EM, Vignali DA, Ziegler SF (2013) Regulatory T cells: recommendations to simplify the nomenclature. Nat Immunol 14(4):307\u2013308. doi:10.1038\/ni.2554","journal-title":"Nat Immunol"},{"issue":"6603","key":"371_CR4","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1038\/383787a0","volume":"383","author":"AK Abbas","year":"1996","unstructured":"Abbas AK, Murphy KM, Sher A (1996) Functional diversity of helper T lymphocytes. Nature 383(6603):787\u2013793","journal-title":"Nature"},{"issue":"8","key":"371_CR5","doi-asserted-by":"publisher","first-page":"e1003678","DOI":"10.1371\/journal.pgen.1003678","volume":"9","author":"DM Absher","year":"2013","unstructured":"Absher DM, Li X, Waite LL, Gibson A, Roberts K, Edberg J, Chatham WW, Kimberly RP (2013) Genome-wide DNA methylation analysis of systemic lupus erythematosus reveals persistent hypomethylation of interferon genes and compositional changes to CD4+ T-cell populations. PLoS Genet 9(8):e1003678. doi:10.1371\/journal.pgen.1003678","journal-title":"PLoS Genet"},{"issue":"9","key":"371_CR6","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1038\/ni1496","volume":"8","author":"EV Acosta-Rodriguez","year":"2007","unstructured":"Acosta-Rodriguez EV, Napolitani G, Lanzavecchia A, Sallusto F (2007a) Interleukins 1beta and 6 but not transforming growth factor-beta are essential for the differentiation of interleukin 17-producing human T helper cells. Nat Immunol 8(9):942\u2013949","journal-title":"Nat Immunol"},{"issue":"6","key":"371_CR7","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/ni1467","volume":"8","author":"EV Acosta-Rodriguez","year":"2007","unstructured":"Acosta-Rodriguez EV, Rivino L, Geginat J, Jarrossay D, Gattorno M, Lanzavecchia A, Sallusto F, Napolitani G (2007b) Surface phenotype and antigenic specificity of human interleukin 17-producing T helper memory cells. Nat Immunol 8(6):639\u2013646","journal-title":"Nat Immunol"},{"issue":"2","key":"371_CR8","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1016\/j.immuni.2010.08.010","volume":"33","author":"PP Ahern","year":"2010","unstructured":"Ahern PP, Schiering C, Buonocore S, McGeachy MJ, Cua DJ, Maloy KJ, Powrie F (2010) Interleukin-23 drives intestinal inflammation through direct activity on T cells. Immunity 33(2):279\u2013288. doi:10.1016\/j.immuni.2010.08.010","journal-title":"Immunity"},{"issue":"3","key":"371_CR9","doi-asserted-by":"publisher","first-page":"1598","DOI":"10.4049\/jimmunol.0803302","volume":"183","author":"AN Ahyi","year":"2009","unstructured":"Ahyi AN, Chang HC, Dent AL, Nutt SL, Kaplan MH (2009) IFN regulatory factor 4 regulates the expression of a subset of Th2 cytokines. J Immunol 183(3):1598\u20131606. doi:10.4049\/jimmunol.0803302","journal-title":"J Immunol"},{"key":"371_CR10","doi-asserted-by":"publisher","DOI":"10.1002\/art.38264","author":"N Altorok","year":"2013","unstructured":"Altorok N, Coit P, Hughes T, Koelsch KA, Stone DU, Rasmussen A, Radfar L, Scofield RH, Sivils KL, Farris AD, Sawalha AH (2013) Genome-wide DNA methylation patterns in naive CD4 T cells from patients with primary Sjogren\u2019s syndrome. Arthritis Rheum. doi:10.1002\/art.38264","journal-title":"Arthritis Rheum"},{"issue":"2","key":"371_CR11","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1016\/j.immuni.2009.06.024","volume":"31","author":"A Androulidaki","year":"2009","unstructured":"Androulidaki A, Iliopoulos D, Arranz A, Doxaki C, Schworer S, Zacharioudaki V, Margioris AN, Tsichlis PN, Tsatsanis C (2009) The kinase Akt1 controls macrophage response to lipopolysaccharide by regulating microRNAs. Immunity 31(2):220\u2013231. doi:10.1016\/j.immuni.2009.06.024","journal-title":"Immunity"},{"issue":"8","key":"371_CR12","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1084\/jem.20070663","volume":"204","author":"F Annunziato","year":"2007","unstructured":"Annunziato F, Cosmi L, Santarlasci V, Maggi L, Liotta F, Mazzinghi B, Parente E, Fili L, Ferri S, Frosali F, Giudici F, Romagnani P, Parronchi P, Tonelli F, Maggi E, Romagnani S (2007) Phenotypic and functional features of human Th17 cells. J Exp Med 204(8):1849\u20131861","journal-title":"J Exp Med"},{"key":"371_CR13","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1146\/annurev.immunol.23.021704.115821","volume":"24","author":"KM Ansel","year":"2006","unstructured":"Ansel KM, Djuretic I, Tanasa B, Rao A (2006) Regulation of Th2 differentiation and Il4 locus accessibility. Annu Rev Immunol 24:607\u2013656. doi:10.1146\/annurev.immunol.23.021704.115821","journal-title":"Annu Rev Immunol"},{"issue":"7","key":"371_CR14","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1038\/ni0703-616","volume":"4","author":"KM Ansel","year":"2003","unstructured":"Ansel KM, Lee DU, Rao A (2003) An epigenetic view of helper T cell differentiation. Nat Immunol 4(7):616\u2013623","journal-title":"Nat Immunol"},{"issue":"7480","key":"371_CR15","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1038\/nature12726","volume":"504","author":"N Arpaia","year":"2013","unstructured":"Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, deRoos P, Liu H, Cross JR, Pfeffer K, Coffer PJ, Rudensky AY (2013) Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504(7480):451\u2013455. doi:10.1038\/nature12726","journal-title":"Nature"},{"issue":"7461","key":"371_CR16","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1038\/nature12331","volume":"500","author":"K Atarashi","year":"2013","unstructured":"Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, Fukuda S, Saito T, Narushima S, Hase K, Kim S, Fritz JV, Wilmes P, Ueha S, Matsushima K, Ohno H, Olle B, Sakaguchi S, Taniguchi T, Morita H, Hattori M, Honda K (2013) Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500(7461):232\u2013236. doi:10.1038\/nature12331","journal-title":"Nature"},{"issue":"6015","key":"371_CR17","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1126\/science.1198469","volume":"331","author":"K Atarashi","year":"2011","unstructured":"Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, Yamasaki S, Saito T, Ohba Y, Taniguchi T, Takeda K, Hori S, Ivanov II, Umesaki Y, Itoh K, Honda K (2011) Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331(6015):337\u2013341. doi:10.1126\/science.1198469","journal-title":"Science"},{"key":"371_CR18","doi-asserted-by":"publisher","first-page":"112","DOI":"10.3389\/fimmu.2013.00112","volume":"4","author":"TM Aune","year":"2013","unstructured":"Aune TM, Collins PL, Collier SP, Henderson MA, Chang S (2013) Epigenetic activation and silencing of the gene that encodes IFN-\u03b3. Front Immunol 4:112. doi:10.3389\/fimmu.2013.00112","journal-title":"Front Immunol"},{"issue":"12","key":"371_CR19","doi-asserted-by":"publisher","first-page":"1380","DOI":"10.1038\/ni1541","volume":"8","author":"A Awasthi","year":"2007","unstructured":"Awasthi A, Carrier Y, Peron JP, Bettelli E, Kamanaka M, Flavell RA, Kuchroo VK, Oukka M, Weiner HL (2007) A dominant function for interleukin 27 in generating interleukin 10-producing anti-inflammatory T cells. Nat Immunol 8(12):1380\u20131389. doi:10.1038\/ni1541","journal-title":"Nat Immunol"},{"issue":"7","key":"371_CR20","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1016\/j.it.2011.04.002","volume":"32","author":"SL Bailey-Bucktrout","year":"2011","unstructured":"Bailey-Bucktrout SL, Bluestone JA (2011) Regulatory T cells: stability revisited. Trends Immunol 32(7):301\u2013306. doi:10.1016\/j.it.2011.04.002","journal-title":"Trends Immunol"},{"issue":"5","key":"371_CR21","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1016\/j.immuni.2013.10.016","volume":"39","author":"SL Bailey-Bucktrout","year":"2013","unstructured":"Bailey-Bucktrout SL, Martinez-Llordella M, Zhou X, Anthony B, Rosenthal W, Luche H, Fehling HJ, Bluestone JA (2013) Self-antigen-driven activation induces instability of regulatory T cells during an inflammatory autoimmune response. Immunity 39 (5):949\u2013962. doi:10.1016\/j.immuni.2013.10.016","journal-title":"Immunity"},{"issue":"5","key":"371_CR22","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1016\/j.immuni.2012.02.012","volume":"36","author":"A Ballesteros-Tato","year":"2012","unstructured":"Ballesteros-Tato A, Leon B, Graf BA, Moquin A, Adams PS, Lund FE, Randall TD (2012) Interleukin-2 inhibits germinal center formation by limiting T follicular helper cell differentiation. Immunity 36(5):847\u2013856. doi:10.1016\/j.immuni.2012.02.012","journal-title":"Immunity"},{"issue":"36","key":"371_CR23","doi-asserted-by":"publisher","first-page":"14532","DOI":"10.1073\/pnas.1212264109","volume":"109","author":"HS Bandukwala","year":"2012","unstructured":"Bandukwala HS, Gagnon J, Togher S, Greenbaum JA, Lamperti ED, Parr NJ, Molesworth AM, Smithers N, Lee K, Witherington J, Tough DF, Prinjha RK, Peters B, Rao A (2012) Selective inhibition of CD4+ T-cell cytokine production and autoimmunity by BET protein and c-Myc inhibitors. Proc Natl Acad Sci USA 109(36):14532\u201314537. doi:10.1073\/pnas.1212264109","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"371_CR24","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1002\/eji.200939381","volume":"40","author":"A Banerjee","year":"2010","unstructured":"Banerjee A, Schambach F, DeJong CS, Hammond SM, Reiner SL (2010) Micro-RNA-155 inhibits IFN-gamma signaling in CD4+ T cells. Eur J Immunol 40(1):225\u2013231. doi:10.1002\/eji.200939381","journal-title":"Eur J Immunol"},{"issue":"9","key":"371_CR25","doi-asserted-by":"crossref","first-page":"2378","DOI":"10.1002\/eji.200737594","volume":"37","author":"U Baron","year":"2007","unstructured":"Baron U, Floess S, Wieczorek G, Baumann K, Grutzkau A, Dong J, Thiel A, Boeld TJ, Hoffmann P, Edinger M, Turbachova I, Hamann A, Olek S, Huehn J (2007) DNA demethylation in the human FOXP3 locus discriminates regulatory T cells from activated FOXP3(+) conventional T cells. Eur J Immunol 37(9):2378\u20132389","journal-title":"Eur J Immunol"},{"issue":"2","key":"371_CR26","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","volume":"116","author":"DP Bartel","year":"2004","unstructured":"Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281\u2013297","journal-title":"Cell"},{"issue":"2","key":"371_CR27","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/j.cell.2009.01.002","volume":"136","author":"DP Bartel","year":"2009","unstructured":"Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215\u2013233. doi:10.1016\/j.cell.2009.01.002","journal-title":"Cell"},{"issue":"2","key":"371_CR28","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1016\/j.smim.2006.01.007","volume":"18","author":"M Battaglia","year":"2006","unstructured":"Battaglia M, Gregori S, Bacchetta R, Roncarolo MG (2006) Tr1 cells: from discovery to their clinical application. Semin Immunol 18(2):120\u2013127. doi:10.1016\/j.smim.2006.01.007","journal-title":"Semin Immunol"},{"issue":"9","key":"371_CR29","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1038\/ni1375","volume":"7","author":"M Batten","year":"2006","unstructured":"Batten M, Li J, Yi S, Kljavin NM, Danilenko DM, Lucas S, Lee J, de Sauvage FJ, Ghilardi N (2006) Interleukin 27 limits autoimmune encephalomyelitis by suppressing the development of interleukin 17-producing T cells. Nat Immunol 7(9):929\u2013936","journal-title":"Nat Immunol"},{"key":"371_CR30","first-page":"471","volume":"42","author":"H Bauer","year":"1963","unstructured":"Bauer H, Horowitz RE, Levenson SM, Popper H (1963) The response of the lymphatic tissue to the microbial flora. Studies on germfree mice. Am J Pathol 42:471\u2013483","journal-title":"Am J Pathol"},{"issue":"9","key":"371_CR31","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1038\/nri3494","volume":"13","author":"D Baumjohann","year":"2013","unstructured":"Baumjohann D, Ansel KM (2013) MicroRNA-mediated regulation of T helper cell differentiation and plasticity. Nat Rev Immunol 13(9):666\u2013678. doi:10.1038\/nri3494","journal-title":"Nat Rev Immunol"},{"issue":"8","key":"371_CR32","doi-asserted-by":"publisher","first-page":"840","DOI":"10.1038\/ni.2642","volume":"14","author":"D Baumjohann","year":"2013","unstructured":"Baumjohann D, Kageyama R, Clingan JM, Morar MM, Patel S, de Kouchkovsky D, Bannard O, Bluestone JA, Matloubian M, Ansel KM, Jeker LT (2013) The microRNA cluster miR-17 approximately 92 promotes TFH cell differentiation and represses subset-inappropriate gene expression. Nat Immunol 14(8):840\u2013848. doi:10.1038\/ni.2642","journal-title":"Nat Immunol"},{"issue":"4","key":"371_CR33","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1016\/j.trsl.2012.02.005","volume":"160","author":"JM Beck","year":"2012","unstructured":"Beck JM, Young VB, Huffnagle GB (2012) The microbiome of the lung. Transl Res 160(4):258\u2013266. doi:10.1016\/j.trsl.2012.02.005","journal-title":"Transl Res"},{"key":"371_CR34","doi-asserted-by":"crossref","unstructured":"Bending D, De La Pena H, Veldhoen M, Phillips JM, Uyttenhove C, Stockinger B, Cooke A (2009) Highly purified Th17 cells from BDC2.5NOD mice convert into Th1-like cells in NOD\/SCID recipient mice. J Clin Investig","DOI":"10.1172\/JCI37865"},{"issue":"1","key":"371_CR35","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1038\/83713","volume":"27","author":"CL Bennett","year":"2001","unstructured":"Bennett CL, Christie J, Ramsdell F, Brunkow ME, Ferguson PJ, Whitesell L, Kelly TE, Saulsbury FT, Chance PF, Ochs HD (2001) The immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome (IPEX) is caused by mutations of FOXP3. Nat Genet 27(1):20\u201321. doi:10.1038\/83713","journal-title":"Nat Genet"},{"issue":"18","key":"371_CR36","doi-asserted-by":"crossref","first-page":"4240","DOI":"10.1182\/blood-2008-10-183251","volume":"113","author":"G Beriou","year":"2009","unstructured":"Beriou G, Costantino CM, Ashley CW, Yang L, Kuchroo VK, Baecher-Allan C, Hafler DA (2009) IL-17-producing human peripheral regulatory T cells retain suppressive function. Blood 113(18):4240\u20134249","journal-title":"Blood"},{"issue":"14","key":"371_CR37","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1101\/gad.1324305","volume":"19","author":"E Bernstein","year":"2005","unstructured":"Bernstein E, Allis CD (2005) RNA meets chromatin. Genes Develop 19(14):1635\u20131655. doi:10.1101\/gad.1324305","journal-title":"Genes Develop"},{"issue":"4","key":"371_CR38","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1016\/0022-2836(88)90122-2","volume":"203","author":"T Bestor","year":"1988","unstructured":"Bestor T, Laudano A, Mattaliano R, Ingram V (1988) Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J Mol Biol 203(4):971\u2013983","journal-title":"J Mol Biol"},{"issue":"7146","key":"371_CR39","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/nature05874","volume":"447","author":"E Birney","year":"2007","unstructured":"Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermuller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaoz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Loytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Xu M, Haidar JN, Yu Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrimsdottir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ (2007) Identification and analysis of functional elements in 1\u00a0% of the human genome by the ENCODE pilot project. Nature 447(7146):799\u2013816. doi:10.1038\/nature05874","journal-title":"Nature"},{"issue":"9","key":"371_CR40","doi-asserted-by":"publisher","first-page":"3280","DOI":"10.1172\/JCI42856","volume":"120","author":"PS Biswas","year":"2010","unstructured":"Biswas PS, Gupta S, Chang E, Song L, Stirzaker RA, Liao JK, Bhagat G, Pernis AB (2010) Phosphorylation of IRF4 by ROCK2 regulates IL-17 and IL-21 production and the development of autoimmunity in mice. J Clin Investig 120(9):3280\u20133295. doi:10.1172\/JCI42856","journal-title":"J Clin Investig"},{"issue":"5","key":"371_CR41","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1002\/art.30281","volume":"63","author":"S Bluml","year":"2011","unstructured":"Bluml S, Bonelli M, Niederreiter B, Puchner A, Mayr G, Hayer S, Koenders MI, van den Berg WB, Smolen J, Redlich K (2011) Essential role of microRNA-155 in the pathogenesis of autoimmune arthritis in mice. Arthritis Rheum 63(5):1281\u20131288. doi:10.1002\/art.30281","journal-title":"Arthritis Rheum"},{"issue":"6","key":"371_CR42","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1084\/jem.20101823","volume":"208","author":"MP Boldin","year":"2011","unstructured":"Boldin MP, Taganov KD, Rao DS, Yang L, Zhao JL, Kalwani M, Garcia-Flores Y, Luong M, Devrekanli A, Xu J, Sun G, Tay J, Linsley PS, Baltimore D (2011) miR-146a is a significant brake on autoimmunity, myeloproliferation, and cancer in mice. J Exp Med 208(6):1189\u20131201. doi:10.1084\/jem.20101823","journal-title":"J Exp Med"},{"key":"371_CR43","doi-asserted-by":"crossref","unstructured":"Boniface K, Blumenschein WM, Brovont-Porth K, McGeachy MJ, Basham B, Desai B, Pierce R, McClanahan TK, Sadekova S, Malefyt RD (2010) Human Th17 Cells Comprise Heterogeneous Subsets including IFN-\u03b3-Producing Cells with Distinct Properties from the Th1 Lineage. J Immunol","DOI":"10.4049\/jimmunol.1000366"},{"issue":"5","key":"371_CR44","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1016\/S1074-7613(00)80388-X","volume":"7","author":"P Brennan","year":"1997","unstructured":"Brennan P, Babbage JW, Burgering BM, Groner B, Reif K, Cantrell DA (1997) Phosphatidylinositol 3-kinase couples the interleukin-2 receptor to the cell cycle regulator E2F. Immunity 7(5):679\u2013689","journal-title":"Immunity"},{"issue":"1","key":"371_CR45","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/83784","volume":"27","author":"ME Brunkow","year":"2001","unstructured":"Brunkow ME, Jeffery EW, Hjerrild KA, Paeper B, Clark LB, Yasayko SA, Wilkinson JE, Galas D, Ziegler SF, Ramsdell F (2001) Disruption of a new forkhead\/winged-helix protein, scurfin, results in the fatal lymphoproliferative disorder of the scurfy mouse. Nat Genet 27(1):68\u201373. doi:10.1038\/83784","journal-title":"Nat Genet"},{"issue":"9","key":"371_CR46","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1038\/ni1500","volume":"8","author":"A Brustle","year":"2007","unstructured":"Brustle A, Heink S, Huber M, Rosenplanter C, Stadelmann C, Yu P, Arpaia E, Mak TW, Kamradt T, Lohoff M (2007) The development of inflammatory T(H)-17 cells requires interferon-regulatory factor 4. Nat Immunol 8(9):958\u2013966. doi:10.1038\/ni1500","journal-title":"Nat Immunol"},{"issue":"10","key":"371_CR47","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1038\/ni.2683","volume":"14","author":"D Burzyn","year":"2013","unstructured":"Burzyn D, Benoist C, Mathis D (2013a) Regulatory T cells in nonlymphoid tissues. Nat Immunol 14(10):1007\u20131013. doi:10.1038\/ni.2683","journal-title":"Nat Immunol"},{"issue":"6","key":"371_CR48","doi-asserted-by":"publisher","first-page":"1282","DOI":"10.1016\/j.cell.2013.10.054","volume":"155","author":"D Burzyn","year":"2013","unstructured":"Burzyn D, Kuswanto W, Kolodin D, Shadrach JL, Cerletti M, Jang Y, Sefik E, Tan TG, Wagers AJ, Benoist C, Mathis D (2013b) A special population of regulatory T cells potentiates muscle repair. Cell 155(6):1282\u20131295. doi:10.1016\/j.cell.2013.10.054","journal-title":"Cell"},{"issue":"18","key":"371_CR49","doi-asserted-by":"publisher","first-page":"1915","DOI":"10.1101\/gad.17446611","volume":"25","author":"MN Cabili","year":"2011","unstructured":"Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915\u20131927. doi:10.1101\/gad.17446611","journal-title":"Genes Dev"},{"issue":"11","key":"371_CR50","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1038\/ng1913","volume":"38","author":"S Cai","year":"2006","unstructured":"Cai S, Lee CC, Kohwi-Shigematsu T (2006) SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nat Genet 38(11):1278\u20131288. doi:10.1038\/ng1913","journal-title":"Nat Genet"},{"issue":"5","key":"371_CR51","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1016\/j.it.2013.01.001","volume":"34","author":"JL Cannons","year":"2013","unstructured":"Cannons JL, Lu KT, Schwartzberg PL (2013) T follicular helper cell diversity and plasticity. Trends Immunol 34(5):200\u2013207. doi:10.1016\/j.it.2013.01.001","journal-title":"Trends Immunol"},{"issue":"5740","key":"371_CR52","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1126\/science.1112014","volume":"309","author":"P Carninci","year":"2005","unstructured":"Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y (2005) The transcriptional landscape of the mammalian genome. Science 309(5740):1559\u20131563. doi:10.1126\/science.1112014","journal-title":"Science"},{"issue":"5955","key":"371_CR53","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1126\/science.1172702","volume":"326","author":"A Chaudhry","year":"2009","unstructured":"Chaudhry A, Rudra D, Treuting P, Samstein RM, Liang Y, Kas A, Rudensky AY (2009) CD4+ regulatory T cells control TH17 responses in a Stat3-dependent manner. Science 326(5955):986\u2013991. doi:10.1126\/science.1172702","journal-title":"Science"},{"issue":"12","key":"371_CR54","doi-asserted-by":"publisher","first-page":"1875","DOI":"10.1084\/jem.20030152","volume":"198","author":"W Chen","year":"2003","unstructured":"Chen W, Jin W, Hardegen N, Lei KJ, Li L, Marinos N, McGrady G, Wahl SM (2003) Conversion of peripheral CD4+\u00a0CD25- naive T cells to CD4+\u00a0CD25+\u00a0regulatory T cells by TGF-beta induction of transcription factor Foxp3. J Exp Med 198(12):1875\u20131886. doi:10.1084\/jem.20030152","journal-title":"J Exp Med"},{"issue":"2","key":"371_CR55","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1016\/j.immuni.2013.08.006","volume":"39","author":"Z Chen","year":"2013","unstructured":"Chen Z, Barbi J, Bu S, Yang HY, Li Z, Gao Y, Jinasena D, Fu J, Lin F, Chen C, Zhang J, Yu N, Li X, Shan Z, Nie J, Gao Z, Tian H, Li Y, Yao Z, Zheng Y, Park BV, Pan Z, Dang E, Wang H, Luo W, Li L, Semenza GL, Zheng SG, Loser K, Tsun A, Greene MI, Pardoll DM, Pan F, Li B (2013) The ubiquitin ligase Stub1 negatively modulates regulatory T cell suppressive activity by promoting degradation of the transcription factor Foxp3. Immunity 39(2):272\u2013285. doi:10.1016\/j.immuni.2013.08.006","journal-title":"Immunity"},{"issue":"9","key":"371_CR56","doi-asserted-by":"crossref","first-page":"2936","DOI":"10.1002\/art.22866","volume":"56","author":"Z Chen","year":"2007","unstructured":"Chen Z, Tato CM, Muul L, Laurence A, O\u2019Shea JJ (2007) Distinct regulation of interleukin-17 in human T helper lymphocytes. Arthritis Rheum 56(9):2936\u20132946","journal-title":"Arthritis Rheum"},{"issue":"1","key":"371_CR57","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1093\/nar\/gkt873","volume":"42","author":"J Choi","year":"2014","unstructured":"Choi J, Jang H, Kim H, Lee JH, Kim ST, Cho EJ, Youn HD (2014) Modulation of lysine methylation in myocyte enhancer factor 2 during skeletal muscle cell differentiation. Nucleic Acids Res 42(1):224\u2013234. doi:10.1093\/nar\/gkt873","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"371_CR58","doi-asserted-by":"publisher","first-page":"2005","DOI":"10.1084\/jem.20081219","volume":"205","author":"MM Chong","year":"2008","unstructured":"Chong MM, Rasmussen JP, Rudensky AY, Littman DR (2008) The RNAseIII enzyme Drosha is critical in T cells for preventing lethal inflammatory disease. J Exp Med 205(9):2005\u20132017. doi:10.1084\/jem.20081219","journal-title":"J Exp Med"},{"issue":"12","key":"371_CR59","doi-asserted-by":"publisher","first-page":"9952","DOI":"10.1074\/jbc.M107694200","volume":"277","author":"GR Christie","year":"2002","unstructured":"Christie GR, Hajduch E, Hundal HS, Proud CG, Taylor PM (2002) Intracellular sensing of amino acids in Xenopus laevis oocytes stimulates p70 S6 kinase in a target of rapamycin-dependent manner. J Biol Chem 277(12):9952\u20139957. doi:10.1074\/jbc.M107694200","journal-title":"J Biol Chem"},{"issue":"8","key":"371_CR60","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1038\/nm.2426","volume":"17","author":"Y Chung","year":"2011","unstructured":"Chung Y, Tanaka S, Chu F, Nurieva RI, Martinez GJ, Rawal S, Wang YH, Lim H, Reynolds JM, Zhou XH, Fan HM, Liu ZM, Neelapu SS, Dong C (2011) Follicular regulatory T cells expressing Foxp3 and Bcl-6 suppress germinal center reactions. Nat Med 17(8):983\u2013988. doi:10.1038\/nm.2426","journal-title":"Nat Med"},{"issue":"7404","key":"371_CR61","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1038\/nature11132","volume":"486","author":"D Cipolletta","year":"2012","unstructured":"Cipolletta D, Feuerer M, Li A, Kamei N, Lee J, Shoelson SE, Benoist C, Mathis D (2012) PPAR-gamma is a major driver of the accumulation and phenotype of adipose tissue Treg cells. Nature 486(7404):549\u2013553. doi:10.1038\/nature11132","journal-title":"Nature"},{"issue":"8","key":"371_CR62","first-page":"3514","volume":"12","author":"EM Coccia","year":"1992","unstructured":"Coccia EM, Cicala C, Charlesworth A, Ciccarelli C, Rossi GB, Philipson L, Sorrentino V (1992) Regulation and expression of a growth arrest-specific gene (gas5) during growth, differentiation, and development. Mol Cell Biol 12(8):3514\u20133521","journal-title":"Mol Cell Biol"},{"issue":"11","key":"371_CR63","doi-asserted-by":"publisher","first-page":"5615","DOI":"10.4049\/jimmunol.1101058","volume":"187","author":"CJ Cohen","year":"2011","unstructured":"Cohen CJ, Crome SQ, MacDonald KG, Dai EL, Mager DL, Levings MK (2011) Human Th1 and Th17 cells exhibit epigenetic stability at signature cytokine and transcription factor loci. J Immunol 187(11):5615\u20135626. doi:10.4049\/jimmunol.1101058","journal-title":"J Immunol"},{"issue":"5","key":"371_CR64","doi-asserted-by":"publisher","first-page":"2084","DOI":"10.4049\/jimmunol.1200774","volume":"189","author":"SP Collier","year":"2012","unstructured":"Collier SP, Collins PL, Williams CL, Boothby MR, Aune TM (2012) Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells. J Immunol 189(5):2084\u20132088. doi:10.4049\/jimmunol.1200774","journal-title":"J Immunol"},{"key":"371_CR65","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1186\/1471-2466-11-29","volume":"11","author":"A Collison","year":"2011","unstructured":"Collison A, Herbert C, Siegle JS, Mattes J, Foster PS, Kumar RK (2011) Altered expression of microRNA in the airway wall in chronic asthma: miR-126 as a potential therapeutic target. BMC Pulm Med 11:29. doi:10.1186\/1471-2466-11-29","journal-title":"BMC Pulm Med"},{"issue":"7169","key":"371_CR66","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1038\/nature06306","volume":"450","author":"LW Collison","year":"2007","unstructured":"Collison LW, Workman CJ, Kuo TT, Boyd K, Wang Y, Vignali KM, Cross R, Sehy D, Blumberg RS, Vignali DA (2007) The inhibitory cytokine IL-35 contributes to regulatory T-cell function. Nature 450(7169):566\u2013569. doi:10.1038\/nature06306","journal-title":"Nature"},{"issue":"8","key":"371_CR67","doi-asserted-by":"publisher","first-page":"1757","DOI":"10.1084\/jem.20070590","volume":"204","author":"JL Coombes","year":"2007","unstructured":"Coombes JL, Siddiqui KR, Arancibia-Carcamo CV, Hall J, Sun CM, Belkaid Y, Powrie F (2007) A functionally specialized population of mucosal CD103+\u00a0DCs induces Foxp3+\u00a0regulatory T cells via a TGF-beta and retinoic acid-dependent mechanism. J Exp Med 204(8):1757\u20131764. doi:10.1084\/jem.20070590","journal-title":"J Exp Med"},{"issue":"1","key":"371_CR68","doi-asserted-by":"publisher","first-page":"120157","DOI":"10.1098\/rsob.120157","volume":"3","author":"SM Coomes","year":"2013","unstructured":"Coomes SM, Pelly VS, Wilson MS (2013) Plasticity within the alphabeta(+)CD4(+) T-cell lineage: when, how and what for? Open Biol 3(1):120157. doi:10.1098\/rsob.120157","journal-title":"Open Biol"},{"issue":"6","key":"371_CR69","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1016\/j.smim.2010.08.001","volume":"22","author":"AE Corcoran","year":"2010","unstructured":"Corcoran AE (2010) The epigenetic role of non-coding RNA transcription and nuclear organization in immunoglobulin repertoire generation. Semin Immunol 22(6):353\u2013361. doi:10.1016\/j.smim.2010.08.001","journal-title":"Semin Immunol"},{"issue":"7","key":"371_CR70","doi-asserted-by":"crossref","first-page":"2197","DOI":"10.4049\/jimmunol.140.7.2197","volume":"140","author":"E Cornacchia","year":"1988","unstructured":"Cornacchia E, Golbus J, Maybaum J, Strahler J, Hanash S, Richardson B (1988) Hydralazine and procainamide inhibit T cell DNA methylation and induce autoreactivity. J Immunol 140(7):2197\u20132200","journal-title":"J Immunol"},{"issue":"2","key":"371_CR71","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/0378-4347(91)80265-E","volume":"566","author":"A Corvetta","year":"1991","unstructured":"Corvetta A, Della Bitta R, Luchetti MM, Pomponio G (1991) 5-Methylcytosine content of DNA in blood, synovial mononuclear cells and synovial tissue from patients affected by autoimmune rheumatic diseases. J Chromatogr 566(2):481\u2013491","journal-title":"J Chromatogr"},{"issue":"8","key":"371_CR72","doi-asserted-by":"publisher","first-page":"2504","DOI":"10.1002\/art.30332","volume":"63","author":"L Cosmi","year":"2011","unstructured":"Cosmi L, Cimaz R, Maggi L, Santarlasci V, Capone M, Borriello F, Frosali F, Querci V, Simonini G, Barra G, Piccinni MP, Liotta F, De Palma R, Maggi E, Romagnani S, Annunziato F (2011) Evidence of the transient nature of the Th17 phenotype of CD4+\u00a0CD161+\u00a0T cells in the synovial fluid of patients with juvenile idiopathic arthritis. Arthritis Rheum 63(8):2504\u20132515. doi:10.1002\/art.30332","journal-title":"Arthritis Rheum"},{"issue":"7","key":"371_CR73","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1016\/j.it.2013.03.002","volume":"34","author":"SQ Crome","year":"2013","unstructured":"Crome SQ, Lang PA, Lang KS, Ohashi PS (2013) Natural killer cells regulate diverse T cell responses. Trends Immunol 34(7):342\u2013349. doi:10.1016\/j.it.2013.03.002","journal-title":"Trends Immunol"},{"key":"371_CR74","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1146\/annurev-immunol-031210-101400","volume":"29","author":"S Crotty","year":"2011","unstructured":"Crotty S (2011) Follicular helper CD4 T cells (TFH). Annu Rev Immunol 29:621\u2013663. doi:10.1146\/annurev-immunol-031210-101400","journal-title":"Annu Rev Immunol"},{"issue":"1","key":"371_CR75","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1111\/j.1600-065X.2012.01117.x","volume":"247","author":"S Crotty","year":"2012","unstructured":"Crotty S (2012) The 1-1-1 fallacy. Immunol Rev 247(1):133\u2013142. doi:10.1111\/j.1600-065X.2012.01117.x","journal-title":"Immunol Rev"},{"issue":"5","key":"371_CR76","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1016\/j.cell.2011.07.033","volume":"146","author":"EV Dang","year":"2011","unstructured":"Dang EV, Barbi J, Yang HY, Jinasena D, Yu H, Zheng Y, Bordman Z, Fu J, Kim Y, Yen HR, Luo W, Zeller K, Shimoda L, Topalian SL, Semenza GL, Dang CV, Pardoll DM, Pan F (2011) Control of T(H)17\/T(reg) balance by hypoxia-inducible factor 1. Cell 146(5):772\u2013784. doi:10.1016\/j.cell.2011.07.033","journal-title":"Cell"},{"issue":"12","key":"371_CR77","doi-asserted-by":"publisher","first-page":"1347","DOI":"10.1038\/ni.1677","volume":"9","author":"V Dardalhon","year":"2008","unstructured":"Dardalhon V, Awasthi A, Kwon H, Galileos G, Gao W, Sobel RA, Mitsdoerffer M, Strom TB, Elyaman W, Ho IC, Khoury S, Oukka M, Kuchroo VK (2008) IL-4 inhibits TGF-beta-induced Foxp3+\u00a0T cells and, together with TGF-beta, generates IL-9+\u00a0IL-10+\u00a0Foxp3(-) effector T cells. Nat Immunol 9(12):1347\u20131355. doi:10.1038\/ni.1677","journal-title":"Nat Immunol"},{"issue":"7466","key":"371_CR78","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1038\/nature12420","volume":"501","author":"E de Wit","year":"2013","unstructured":"de Wit E, Bouwman BA, Zhu Y, Klous P, Splinter E, Verstegen MJ, Krijger PH, Festuccia N, Nora EP, Welling M, Heard E, Geijsen N, Poot RA, Chambers I, de Laat W (2013) The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature 501(7466):227\u2013231. doi:10.1038\/nature12420","journal-title":"Nature"},{"issue":"2","key":"371_CR79","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1016\/j.immuni.2010.07.015","volume":"33","author":"EK Deenick","year":"2010","unstructured":"Deenick EK, Chan A, Ma CS, Gatto D, Schwartzberg PL, Brink R, Tangye SG (2010) Follicular helper T cell differentiation requires continuous antigen presentation that is independent of unique B cell signaling. Immunity 33(2):241\u2013253. doi:10.1016\/j.immuni.2010.07.015","journal-title":"Immunity"},{"issue":"6","key":"371_CR80","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1016\/j.immuni.2009.04.014","volume":"30","author":"GM Delgoffe","year":"2009","unstructured":"Delgoffe GM, Kole TP, Zheng Y, Zarek PE, Matthews KL, Xiao B, Worley PF, Kozma SC, Powell JD (2009) The mTOR kinase differentially regulates effector and regulatory T cell lineage commitment. Immunity 30(6):832\u2013844. doi:10.1016\/j.immuni.2009.04.014","journal-title":"Immunity"},{"issue":"4","key":"371_CR81","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1038\/ni.2005","volume":"12","author":"GM Delgoffe","year":"2011","unstructured":"Delgoffe GM, Pollizzi KN, Waickman AT, Heikamp E, Meyers DJ, Horton MR, Xiao B, Worley PF, Powell JD (2011) The kinase mTOR regulates the differentiation of helper T cells through the selective activation of signaling by mTORC1 and mTORC2. Nat Immunol 12(4):295\u2013303. doi:10.1038\/ni.2005","journal-title":"Nat Immunol"},{"issue":"7466","key":"371_CR82","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1038\/nature12428","volume":"501","author":"GM Delgoffe","year":"2013","unstructured":"Delgoffe GM, Woo SR, Turnis ME, Gravano DM, Guy C, Overacre AE, Bettini ML, Vogel P, Finkelstein D, Bonnevier J, Workman CJ, Vignali DA (2013) Stability and function of regulatory T cells is maintained by a neuropilin-1-semaphorin-4a axis. Nature 501(7466):252\u2013256. doi:10.1038\/nature12428","journal-title":"Nature"},{"issue":"5","key":"371_CR83","doi-asserted-by":"publisher","first-page":"602","DOI":"10.1016\/j.stem.2013.08.013","volume":"13","author":"M Denholtz","year":"2013","unstructured":"Denholtz M, Bonora G, Chronis C, Splinter E, de Laat W, Ernst J, Pellegrini M, Plath K (2013) Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell 13(5):602\u2013616. doi:10.1016\/j.stem.2013.08.013","journal-title":"Cell Stem Cell"},{"issue":"9","key":"371_CR84","doi-asserted-by":"publisher","first-page":"1775","DOI":"10.1101\/gr.132159.111","volume":"22","author":"T Derrien","year":"2012","unstructured":"Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigo R (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775\u20131789. doi:10.1101\/gr.132159.111","journal-title":"Genome Res"},{"issue":"7398","key":"371_CR85","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature11082","volume":"485","author":"JR Dixon","year":"2012","unstructured":"Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376\u2013380. doi:10.1038\/nature11082","journal-title":"Nature"},{"issue":"7414","key":"371_CR86","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/nature11233","volume":"489","author":"S Djebali","year":"2012","unstructured":"Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Roder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigo R, Gingeras TR (2012) Landscape of transcription in human cells. Nature 489(7414):101\u2013108. doi:10.1038\/nature11233","journal-title":"Nature"},{"issue":"1","key":"371_CR87","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3858\/emm.2011.43.1.007","volume":"43","author":"C Dong","year":"2011","unstructured":"Dong C (2011) Genetic controls of Th17 cell differentiation and plasticity. Exp Mol Med 43(1):1\u20136. doi:10.3858\/emm.2011.43.1.007","journal-title":"Exp Mol Med"},{"issue":"8","key":"371_CR88","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1038\/ni.1767","volume":"10","author":"T Duhen","year":"2009","unstructured":"Duhen T, Geiger R, Jarrossay D, Lanzavecchia A, Sallusto F (2009) Production of interleukin 22 but not interleukin 17 by a subset of human skin-homing memory T cells. Nat Immunol 10(8):857\u2013863. doi:10.1038\/ni.1767","journal-title":"Nat Immunol"},{"issue":"3","key":"371_CR89","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1016\/j.jaci.2012.09.025","volume":"131","author":"KR Engelhardt","year":"2013","unstructured":"Engelhardt KR, Shah N, Faizura-Yeop I, Kocacik Uygun DF, Frede N, Muise AM, Shteyer E, Filiz S, Chee R, Elawad M, Hartmann B, Arkwright PD, Dvorak C, Klein C, Puck JM, Grimbacher B, Glocker EO (2013) Clinical outcome in IL-10- and IL-10 receptor-deficient patients with or without hematopoietic stem cell transplantation. J Allergy Clin Immunol 131(3):825\u2013830. doi:10.1016\/j.jaci.2012.09.025","journal-title":"J Allergy Clin Immunol"},{"issue":"6","key":"371_CR90","doi-asserted-by":"publisher","first-page":"4017","DOI":"10.1167\/iovs.13-11937","volume":"54","author":"T Escobar","year":"2013","unstructured":"Escobar T, Yu CR, Muljo SA, Egwuagu CE (2013) STAT3 activates miR-155 in Th17 cells and acts in concert to promote experimental autoimmune uveitis. Invest Ophthalmol Vis Sci 54(6):4017\u20134025. doi:10.1167\/iovs.13-11937","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"3","key":"371_CR91","doi-asserted-by":"publisher","first-page":"e17739","DOI":"10.1371\/journal.pone.0017739","volume":"6","author":"D Eto","year":"2011","unstructured":"Eto D, Lao C, DiToro D, Barnett B, Escobar TC, Kageyama R, Yusuf I, Crotty S (2011) IL-21 and IL-6 are critical for different aspects of B cell immunity and redundantly induce optimal follicular helper CD4 T cell (Tfh) differentiation. PLoS ONE 6(3):e17739. doi:10.1371\/journal.pone.0017739","journal-title":"PLoS ONE"},{"key":"371_CR92","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1146\/annurev-biochem-060308-103103","volume":"79","author":"MR Fabian","year":"2010","unstructured":"Fabian MR, Sonenberg N, Filipowicz W (2010) Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79:351\u2013379. doi:10.1146\/annurev-biochem-060308-103103","journal-title":"Annu Rev Biochem"},{"issue":"2","key":"371_CR93","doi-asserted-by":"crossref","first-page":"e38","DOI":"10.1371\/journal.pbio.0050038","volume":"5","author":"S Floess","year":"2007","unstructured":"Floess S, Freyer J, Siewert C, Baron U, Olek S, Polansky J, Schlawe K, Chang HD, Bopp T, Schmitt E, Klein-Hessling S, Serfling E, Hamann A, Huehn J (2007) Epigenetic control of the foxp3 locus in regulatory T cells. PLoS Biol 5(2):e38","journal-title":"PLoS Biol"},{"issue":"4","key":"371_CR94","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1038\/ni904","volume":"4","author":"JD Fontenot","year":"2003","unstructured":"Fontenot JD, Gavin MA, Rudensky AY (2003) Foxp3 programs the development and function of CD4+\u00a0CD25+\u00a0regulatory T cells. Nat Immunol 4(4):330\u2013336. doi:10.1038\/ni904","journal-title":"Nat Immunol"},{"issue":"11","key":"371_CR95","doi-asserted-by":"publisher","first-page":"844","DOI":"10.1038\/nri1710","volume":"5","author":"CJ Fox","year":"2005","unstructured":"Fox CJ, Hammerman PS, Thompson CB (2005) Fuel feeds function: energy metabolism and the T-cell response. Nat Rev Immunol 5(11):844\u2013852. doi:10.1038\/nri1710","journal-title":"Nat Rev Immunol"},{"issue":"10","key":"371_CR96","doi-asserted-by":"publisher","first-page":"972","DOI":"10.1038\/ni.2420","volume":"13","author":"W Fu","year":"2012","unstructured":"Fu W, Ergun A, Lu T, Hill JA, Haxhinasto S, Fassett MS, Gazit R, Adoro S, Glimcher L, Chan S, Kastner P, Rossi D, Collins JJ, Mathis D, Benoist C (2012) A multiply redundant genetic switch \u2018locks in\u2019 the transcriptional signature of regulatory T cells. Nat Immunol 13(10):972\u2013980. doi:10.1038\/ni.2420","journal-title":"Nat Immunol"},{"issue":"7480","key":"371_CR97","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1038\/nature12721","volume":"504","author":"Y Furusawa","year":"2013","unstructured":"Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, Nakanishi Y, Uetake C, Kato K, Kato T, Takahashi M, Fukuda NN, Murakami S, Miyauchi E, Hino S, Atarashi K, Onawa S, Fujimura Y, Lockett T, Clarke JM, Topping DL, Tomita M, Hori S, Ohara O, Morita T, Koseki H, Kikuchi J, Honda K, Hase K, Ohno H (2013) Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504(7480):446\u2013450. doi:10.1038\/nature12721","journal-title":"Nature"},{"issue":"4","key":"371_CR98","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1016\/j.immuni.2009.08.020","volume":"31","author":"V Gaboriau-Routhiau","year":"2009","unstructured":"Gaboriau-Routhiau V, Rakotobe S, Lecuyer E, Mulder I, Lan A, Bridonneau C, Rochet V, Pisi A, De Paepe M, Brandi G, Eberl G, Snel J, Kelly D, Cerf-Bensussan N (2009) The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 31(4):677\u2013689. doi:10.1016\/j.immuni.2009.08.020","journal-title":"Immunity"},{"issue":"6","key":"371_CR99","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1038\/nm.3179","volume":"19","author":"N Gagliani","year":"2013","unstructured":"Gagliani N, Magnani CF, Huber S, Gianolini ME, Pala M, Licona-Limon P, Guo B, Herbert DR, Bulfone A, Trentini F, Di Serio C, Bacchetta R, Andreani M, Brockmann L, Gregori S, Flavell RA, Roncarolo MG (2013) Coexpression of CD49b and LAG-3 identifies human and mouse T regulatory type 1 cells. Nat Med 19(6):739\u2013746. doi:10.1038\/nm.3179","journal-title":"Nat Med"},{"issue":"3","key":"371_CR100","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1042\/BJ20081668","volume":"416","author":"JM Garcia-Martinez","year":"2008","unstructured":"Garcia-Martinez JM, Alessi DR (2008) mTOR complex 2 (mTORC2) controls hydrophobic motif phosphorylation and activation of serum- and glucocorticoid-induced protein kinase 1 (SGK1). Biochem J 416(3):375\u2013385. doi:10.1042\/BJ20081668","journal-title":"Biochem J"},{"issue":"5","key":"371_CR101","doi-asserted-by":"publisher","first-page":"794","DOI":"10.1016\/j.immuni.2011.03.021","volume":"34","author":"MB Geuking","year":"2011","unstructured":"Geuking MB, Cahenzli J, Lawson MA, Ng DC, Slack E, Hapfelmeier S, McCoy KD, Macpherson AJ (2011) Intestinal bacterial colonization induces mutualistic regulatory T cell responses. Immunity 34(5):794\u2013806. doi:10.1016\/j.immuni.2011.03.021","journal-title":"Immunity"},{"issue":"3","key":"371_CR102","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1016\/j.immuni.2010.02.008","volume":"32","author":"S Ghisletti","year":"2010","unstructured":"Ghisletti S, Barozzi I, Mietton F, Polletti S, De Santa F, Venturini E, Gregory L, Lonie L, Chew A, Wei CL, Ragoussis J, Natoli G (2010) Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 32(3):317\u2013328. doi:10.1016\/j.immuni.2010.02.008","journal-title":"Immunity"},{"key":"371_CR103","doi-asserted-by":"crossref","unstructured":"Ghoreschi K, Laurence A, Yang XP, Tato CM, McGeachy MJ, Konkel JE, Ramos HL, Wei L, Davidson TS, Bouladoux N, Grainger JR, Chen Q, Kanno Y, Watford WT, Sun HW, Eberl G, Shevach EM, Belkaid Y, Cua DJ, Chen W, O\u2019Shea JJ (2010) Generation of pathogenic T(H)17 cells in the absence of TGF-beta signalling. Nature 467 (7318):967\u2013971","DOI":"10.1038\/nature09447"},{"issue":"5","key":"371_CR104","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1016\/j.molcel.2013.02.011","volume":"49","author":"JH Gibcus","year":"2013","unstructured":"Gibcus JH, Dekker J (2013) The hierarchy of the 3D genome. Mol Cell 49(5):773\u2013782. doi:10.1016\/j.molcel.2013.02.011","journal-title":"Mol Cell"},{"issue":"5","key":"371_CR105","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1084\/jem.20090303","volume":"206","author":"A Glatman Zaretsky","year":"2009","unstructured":"Glatman Zaretsky A, Taylor JJ, King IL, Marshall FA, Mohrs M, Pearce EJ (2009) T follicular helper cells differentiate from Th2 cells in response to helminth antigens. J Exp Med 206(5):991\u2013999. doi:10.1084\/jem.20090303","journal-title":"J Exp Med"},{"issue":"21","key":"371_CR106","doi-asserted-by":"publisher","first-page":"2033","DOI":"10.1056\/NEJMoa0907206","volume":"361","author":"EO Glocker","year":"2009","unstructured":"Glocker EO, Kotlarz D, Boztug K, Gertz EM, Schaffer AA, Noyan F, Perro M, Diestelhorst J, Allroth A, Murugan D, Hatscher N, Pfeifer D, Sykora KW, Sauer M, Kreipe H, Lacher M, Nustede R, Woellner C, Baumann U, Salzer U, Koletzko S, Shah N, Segal AW, Sauerbrey A, Buderus S, Snapper SB, Grimbacher B, Klein C (2009) Inflammatory bowel disease and mutations affecting the interleukin-10 receptor. N Engl J Med 361(21):2033\u20132045. doi:10.1056\/NEJMoa0907206","journal-title":"N Engl J Med"},{"issue":"3","key":"371_CR107","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.4049\/jimmunol.1100853","volume":"187","author":"R Goenka","year":"2011","unstructured":"Goenka R, Barnett LG, Silver JS, O\u2019Neill PJ, Hunter CA, Cancro MP, Laufer TM (2011) Cutting edge: dendritic cell-restricted antigen presentation initiates the follicular helper T cell program but cannot complete ultimate effector differentiation. J Immunol 187(3):1091\u20131095. doi:10.4049\/jimmunol.1100853","journal-title":"J Immunol"},{"key":"371_CR108","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1146\/annurev.biochem.74.010904.153721","volume":"74","author":"MG Goll","year":"2005","unstructured":"Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74:481\u2013514. doi:10.1146\/annurev.biochem.74.010904.153721","journal-title":"Annu Rev Biochem"},{"issue":"4","key":"371_CR109","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1016\/j.cell.2013.01.015","volume":"152","author":"JA Gomez","year":"2013","unstructured":"Gomez JA, Wapinski OL, Yang YW, Bureau JF, Gopinath S, Monack DM, Chang HY, Brahic M, Kirkegaard K (2013) The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus. Cell 152(4):743\u2013754. doi:10.1016\/j.cell.2013.01.015","journal-title":"Cell"},{"issue":"2","key":"371_CR110","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1016\/j.ccr.2007.07.006","volume":"12","author":"JD Gordan","year":"2007","unstructured":"Gordan JD, Thompson CB, Simon MC (2007) HIF and c-Myc: sibling rivals for control of cancer cell metabolism and proliferation. Cancer Cell 12(2):108\u2013113. doi:10.1016\/j.ccr.2007.07.006","journal-title":"Cancer Cell"},{"key":"371_CR111","doi-asserted-by":"publisher","first-page":"30","DOI":"10.3389\/fimmu.2012.00030","volume":"3","author":"S Gregori","year":"2012","unstructured":"Gregori S, Goudy KS, Roncarolo MG (2012) The cellular and molecular mechanisms of immuno-suppression by human type 1 regulatory T cells. Front Immunol 3:30. doi:10.3389\/fimmu.2012.00030","journal-title":"Front Immunol"},{"issue":"5931","key":"371_CR112","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1126\/science.1171700","volume":"324","author":"EA Grice","year":"2009","unstructured":"Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA (2009) Topographical and temporal diversity of the human skin microbiome. Science 324(5931):1190\u20131192. doi:10.1126\/science.1171700","journal-title":"Science"},{"issue":"6","key":"371_CR113","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1016\/j.devcel.2006.10.007","volume":"11","author":"DA Guertin","year":"2006","unstructured":"Guertin DA, Stevens DM, Thoreen CC, Burds AA, Kalaany NY, Moffat J, Brown M, Fitzgerald KJ, Sabatini DM (2006) Ablation in mice of the mTORC components raptor, rictor, or mLST8 reveals that mTORC2 is required for signaling to Akt-FOXO and PKCalpha, but not S6K1. Dev Cell 11(6):859\u2013871. doi:10.1016\/j.devcel.2006.10.007","journal-title":"Dev Cell"},{"issue":"7235","key":"371_CR114","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1038\/nature07672","volume":"458","author":"M Guttman","year":"2009","unstructured":"Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458(7235):223\u2013227. doi:10.1038\/nature07672","journal-title":"Nature"},{"issue":"7364","key":"371_CR115","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1038\/nature10398","volume":"477","author":"M Guttman","year":"2011","unstructured":"Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477(7364):295\u2013300. doi:10.1038\/nature10398","journal-title":"Nature"},{"issue":"2","key":"371_CR116","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.molcel.2008.03.003","volume":"30","author":"DM Gwinn","year":"2008","unstructured":"Gwinn DM, Shackelford DB, Egan DF, Mihaylova MM, Mery A, Vasquez DS, Turk BE, Shaw RJ (2008) AMPK phosphorylation of raptor mediates a metabolic checkpoint. Mol Cell 30(2):214\u2013226. doi:10.1016\/j.molcel.2008.03.003","journal-title":"Mol Cell"},{"issue":"7253","key":"371_CR117","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1038\/nature08079","volume":"460","author":"S Hadjur","year":"2009","unstructured":"Hadjur S, Williams LM, Ryan NK, Cobb BS, Sexton T, Fraser P, Fisher AG, Merkenschlager M (2009) Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus. Nature 460(7253):410\u2013413. doi:10.1038\/nature08079","journal-title":"Nature"},{"issue":"4","key":"371_CR118","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1016\/j.immuni.2008.08.009","volume":"29","author":"JA Hall","year":"2008","unstructured":"Hall JA, Bouladoux N, Sun CM, Wohlfert EA, Blank RB, Zhu Q, Grigg ME, Berzofsky JA, Belkaid Y (2008) Commensal DNA limits regulatory T cell conversion and is a natural adjuvant of intestinal immune responses. Immunity 29(4):637\u2013649. doi:10.1016\/j.immuni.2008.08.009","journal-title":"Immunity"},{"issue":"6101","key":"371_CR119","doi-asserted-by":"publisher","first-page":"1553","DOI":"10.1126\/science.1220961","volume":"337","author":"TW Hand","year":"2012","unstructured":"Hand TW, Dos Santos LM, Bouladoux N, Molloy MJ, Pagan AJ, Pepper M, Maynard CL, Elson CO 3rd, Belkaid Y (2012) Acute gastrointestinal infection induces long-lived microbiota-specific T cell responses. Science 337(6101):1553\u20131556. doi:10.1126\/science.1220961","journal-title":"Science"},{"issue":"7441","key":"371_CR120","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1038\/nature11993","volume":"495","author":"TB Hansen","year":"2013","unstructured":"Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495(7441):384\u2013388. doi:10.1038\/nature11993","journal-title":"Nature"},{"issue":"11","key":"371_CR121","doi-asserted-by":"publisher","first-page":"2001","DOI":"10.1084\/jem.20111497","volume":"209","author":"W Hansen","year":"2012","unstructured":"Hansen W, Hutzler M, Abel S, Alter C, Stockmann C, Kliche S, Albert J, Sparwasser T, Sakaguchi S, Westendorf AM, Schadendorf D, Buer J, Helfrich I (2012) Neuropilin 1 deficiency on CD4+\u00a0Foxp3+\u00a0regulatory T cells impairs mouse melanoma growth. J Exp Med 209(11):2001\u20132016. doi:10.1084\/jem.20111497","journal-title":"J Exp Med"},{"issue":"2","key":"371_CR122","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1016\/j.immuni.2012.02.002","volume":"36","author":"Y Harada","year":"2012","unstructured":"Harada Y, Tanaka S, Motomura Y, Ohno S, Yanagi Y, Inoue H, Kubo M (2012) The 3\u2032 enhancer CNS2 is a critical regulator of interleukin-4-mediated humoral immunity in follicular helper T cells. Immunity 36(2):188\u2013200. doi:10.1016\/j.immuni.2012.02.002","journal-title":"Immunity"},{"issue":"6057","key":"371_CR123","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1126\/science.1208421","volume":"334","author":"JA Harker","year":"2011","unstructured":"Harker JA, Lewis GM, Mack L, Zuniga EI (2011) Late interleukin-6 escalates T follicular helper cell responses and controls a chronic viral infection. Science 334(6057):825\u2013829. doi:10.1126\/science.1208421","journal-title":"Science"},{"key":"371_CR124","doi-asserted-by":"crossref","unstructured":"Hegazy AN, Peine M, Helmstetter C, Panse I, Frohlich A, Bergthaler A, Flatz L, Pinschewer DD, Radbruch A, Lohning M (2010) Interferons direct Th2 cell reprogramming to generate a stable GATA-3(+)T-bet(+) cell subset with combined Th2 and Th1 cell functions. Immunity 32 (1):116\u2013128","DOI":"10.1016\/j.immuni.2009.12.004"},{"issue":"7243","key":"371_CR125","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1038\/nature07829","volume":"459","author":"ND Heintzman","year":"2009","unstructured":"Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459(7243):108\u2013112. doi:10.1038\/nature07829","journal-title":"Nature"},{"issue":"4","key":"371_CR126","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","volume":"38","author":"S Heinz","year":"2010","unstructured":"Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38(4):576\u2013589. doi:10.1016\/j.molcel.2010.05.004","journal-title":"Mol Cell"},{"issue":"3","key":"371_CR127","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1111\/j.1365-2567.2011.03483.x","volume":"134","author":"K Hirahara","year":"2011","unstructured":"Hirahara K, Vahedi G, Ghoreschi K, Yang XP, Nakayamada S, Kanno Y, O\u2019Shea JJ, Laurence A (2011) Helper T-cell differentiation and plasticity: insights from epigenetics. Immunology 134(3):235\u2013245. doi:10.1111\/j.1365-2567.2011.03483.x","journal-title":"Immunology"},{"issue":"3","key":"371_CR128","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1038\/nri2710","volume":"10","author":"LV Hooper","year":"2010","unstructured":"Hooper LV, Macpherson AJ (2010) Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat Rev Immunol 10(3):159\u2013169. doi:10.1038\/nri2710","journal-title":"Nat Rev Immunol"},{"issue":"7","key":"371_CR129","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1016\/j.it.2011.04.004","volume":"32","author":"S Hori","year":"2011","unstructured":"Hori S (2011) Regulatory T cell plasticity: beyond the controversies. Trends Immunol 32(7):295\u2013300. doi:10.1016\/j.it.2011.04.004","journal-title":"Trends Immunol"},{"issue":"5609","key":"371_CR130","doi-asserted-by":"publisher","first-page":"1057","DOI":"10.1126\/science.1079490","volume":"299","author":"S Hori","year":"2003","unstructured":"Hori S, Nomura T, Sakaguchi S (2003) Control of regulatory T cell development by the transcription factor Foxp3. Science 299(5609):1057\u20131061. doi:10.1126\/science.1079490","journal-title":"Science"},{"issue":"9","key":"371_CR131","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/j.it.2008.06.005","volume":"29","author":"DA Horwitz","year":"2008","unstructured":"Horwitz DA, Zheng SG, Gray JD (2008) Natural and TGF-beta-induced Foxp3(+)CD4(+) CD25(+) regulatory T cells are not mirror images of each other. Trends Immunol 29(9):429\u2013435","journal-title":"Trends Immunol"},{"issue":"11","key":"371_CR132","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1038\/ni.2712","volume":"14","author":"G Hu","year":"2013","unstructured":"Hu G, Tang Q, Sharma S, Yu F, Escobar TM, Muljo SA, Zhu J, Zhao K (2013a) Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation. Nat Immunol 14(11):1190\u20131198. doi:10.1038\/ni.2712","journal-title":"Nat Immunol"},{"issue":"12","key":"371_CR133","doi-asserted-by":"publisher","first-page":"5972","DOI":"10.4049\/jimmunol.1300351","volume":"190","author":"R Hu","year":"2013","unstructured":"Hu R, Huffaker TB, Kagele DA, Runtsch MC, Bake E, Chaudhuri AA, Round JL, O\u2019Connell RM (2013b) MicroRNA-155 confers encephalogenic potential to Th17 cells by promoting effector gene expression. J Immunol 190(12):5972\u20135980. doi:10.4049\/jimmunol.1300351","journal-title":"J Immunol"},{"issue":"52","key":"371_CR134","doi-asserted-by":"publisher","first-page":"20846","DOI":"10.1073\/pnas.0809077106","volume":"105","author":"M Huber","year":"2008","unstructured":"Huber M, Brustle A, Reinhard K, Guralnik A, Walter G, Mahiny A, von Low E, Lohoff M (2008) IRF4 is essential for IL-21-mediated induction, amplification, and stabilization of the Th17 phenotype. Proc Natl Acad Sci USA 105(52):20846\u201320851. doi:10.1073\/pnas.0809077106","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"371_CR135","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1038\/nri2474","volume":"9","author":"J Huehn","year":"2009","unstructured":"Huehn J, Polansky JK, Hamann A (2009) Epigenetic control of FOXP3 expression: the key to a stable regulatory T-cell lineage? Nat Rev Immunol 9(2):83\u201389. doi:10.1038\/nri2474","journal-title":"Nat Rev Immunol"},{"issue":"6","key":"371_CR136","doi-asserted-by":"publisher","first-page":"1697","DOI":"10.1016\/j.celrep.2012.10.025","volume":"2","author":"TB Huffaker","year":"2012","unstructured":"Huffaker TB, Hu R, Runtsch MC, Bake E, Chen X, Zhao J, Round JL, Baltimore D, O\u2019Connell RM (2012) Epistasis between microRNAs 155 and 146a during T cell-mediated antitumor immunity. Cell Rep 2(6):1697\u20131709. doi:10.1016\/j.celrep.2012.10.025","journal-title":"Cell Rep"},{"issue":"9","key":"371_CR137","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1084\/jem.20051044","volume":"202","author":"ES Hwang","year":"2005","unstructured":"Hwang ES, Hong JH, Glimcher LH (2005a) IL-2 production in developing Th1 cells is regulated by heterodimerization of RelA and T-bet and requires T-bet serine residue 508. J Exp Med 202(9):1289\u20131300. doi:10.1084\/jem.20051044","journal-title":"J Exp Med"},{"issue":"5708","key":"371_CR138","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1126\/science.1103336","volume":"307","author":"ES Hwang","year":"2005","unstructured":"Hwang ES, Szabo SJ, Schwartzberg PL, Glimcher LH (2005b) T helper cell fate specified by kinase-mediated interaction of T-bet with GATA-3. Science 307(5708):430\u2013433. doi:10.1126\/science.1103336","journal-title":"Science"},{"issue":"4","key":"371_CR139","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.cell.2011.10.002","volume":"147","author":"NT Ingolia","year":"2011","unstructured":"Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147(4):789\u2013802. doi:10.1016\/j.cell.2011.10.002","journal-title":"Cell"},{"issue":"3","key":"371_CR140","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","volume":"139","author":"II Ivanov","year":"2009","unstructured":"Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, Wei D, Goldfarb KC, Santee CA, Lynch SV, Tanoue T, Imaoka A, Itoh K, Takeda K, Umesaki Y, Honda K, Littman DR (2009) Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139(3):485\u2013498. doi:10.1016\/j.cell.2009.09.033","journal-title":"Cell"},{"issue":"4","key":"371_CR141","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.chom.2008.09.009","volume":"4","author":"II Ivanov","year":"2008","unstructured":"Ivanov II, Frutos Rde L, Manel N, Yoshinaga K, Rifkin DB, Sartor RB, Finlay BB, Littman DR (2008) Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 4(4):337\u2013349. doi:10.1016\/j.chom.2008.09.009","journal-title":"Cell Host Microbe"},{"issue":"11","key":"371_CR142","doi-asserted-by":"publisher","first-page":"5764","DOI":"10.4049\/jimmunol.1203403","volume":"190","author":"EJ Jang","year":"2013","unstructured":"Jang EJ, Park HR, Hong JH, Hwang ES (2013) Lysine 313 of T-box is crucial for modulation of protein stability, DNA binding, and threonine phosphorylation of T-bet. J Immunol 190(11):5764\u20135770. doi:10.4049\/jimmunol.1203403","journal-title":"J Immunol"},{"issue":"2","key":"371_CR143","doi-asserted-by":"crossref","first-page":"e1612","DOI":"10.1371\/journal.pone.0001612","volume":"3","author":"PC Janson","year":"2008","unstructured":"Janson PC, Winerdal ME, Marits P, Thorn M, Ohlsson R, Winqvist O (2008) FOXP3 promoter demethylation reveals the committed Treg population in humans. PLoS ONE 3(2):e1612","journal-title":"PLoS ONE"},{"issue":"7475","key":"371_CR144","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nature12644","volume":"503","author":"F Jin","year":"2013","unstructured":"Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B (2013) A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503(7475):290\u2013294. doi:10.1038\/nature12644","journal-title":"Nature"},{"issue":"2","key":"371_CR145","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1084\/jem.20111174","volume":"209","author":"RJ Johnston","year":"2012","unstructured":"Johnston RJ, Choi YS, Diamond JA, Yang JA, Crotty S (2012) STAT5 is a potent negative regulator of TFH cell differentiation. J Exp Med 209(2):243\u2013250. doi:10.1084\/jem.20111174","journal-title":"J Exp Med"},{"issue":"5943","key":"371_CR146","doi-asserted-by":"publisher","first-page":"1006","DOI":"10.1126\/science.1175870","volume":"325","author":"RJ Johnston","year":"2009","unstructured":"Johnston RJ, Poholek AC, DiToro D, Yusuf I, Eto D, Barnett B, Dent AL, Craft J, Crotty S (2009) Bcl6 and Blimp-1 are reciprocal and antagonistic regulators of T follicular helper cell differentiation. Science 325(5943):1006\u20131010. doi:10.1126\/science.1175870","journal-title":"Science"},{"issue":"5\u20136","key":"371_CR147","doi-asserted-by":"publisher","first-page":"391","DOI":"10.2119\/molmed.2011.00058","volume":"17","author":"LA Joosten","year":"2011","unstructured":"Joosten LA, Leoni F, Meghji S, Mascagni P (2011) Inhibition of HDAC activity by ITF2357 ameliorates joint inflammation and prevents cartilage and bone destruction in experimental arthritis. Mol Med 17(5\u20136):391\u2013396. doi:10.2119\/molmed.2011.00058","journal-title":"Mol Med"},{"issue":"23","key":"371_CR148","doi-asserted-by":"publisher","first-page":"3738","DOI":"10.1016\/j.febslet.2011.03.052","volume":"585","author":"A Junker","year":"2011","unstructured":"Junker A (2011) Pathophysiology of translational regulation by microRNAs in multiple sclerosis. FEBS Lett 585(23):3738\u20133746. doi:10.1016\/j.febslet.2011.03.052","journal-title":"FEBS Lett"},{"issue":"1","key":"371_CR149","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1038\/83144","volume":"2","author":"LP Kane","year":"2001","unstructured":"Kane LP, Andres PG, Howland KC, Abbas AK, Weiss A (2001) Akt provides the CD28 costimulatory signal for up-regulation of IL-2 and IFN-gamma but not TH2 cytokines. Nat Immunol 2(1):37\u201344. doi:10.1038\/83144","journal-title":"Nat Immunol"},{"key":"371_CR150","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1146\/annurev-immunol-020711-075058","volume":"30","author":"Y Kanno","year":"2012","unstructured":"Kanno Y, Vahedi G, Hirahara K, Singleton K, O\u2019Shea JJ (2012) Transcriptional and epigenetic control of T helper cell specification: molecular mechanisms underlying commitment and plasticity. Annu Rev Immunol 30:707\u2013731. doi:10.1146\/annurev-immunol-020711-075058","journal-title":"Annu Rev Immunol"},{"issue":"5830","key":"371_CR151","doi-asserted-by":"publisher","first-page":"1484","DOI":"10.1126\/science.1138341","volume":"316","author":"P Kapranov","year":"2007","unstructured":"Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316(5830):1484\u20131488. doi:10.1126\/science.1138341","journal-title":"Science"},{"issue":"28","key":"371_CR152","doi-asserted-by":"publisher","first-page":"11667","DOI":"10.1073\/pnas.0904715106","volume":"106","author":"AM Khalil","year":"2009","unstructured":"Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 106(28):11667\u201311672. doi:10.1073\/pnas.0904715106","journal-title":"Proc Natl Acad Sci USA"},{"issue":"7","key":"371_CR153","doi-asserted-by":"publisher","first-page":"1507","DOI":"10.1016\/j.cell.2013.11.039","volume":"155","author":"KR Kieffer-Kwon","year":"2013","unstructured":"Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grontved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R (2013) Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 155(7):1507\u20131520. doi:10.1016\/j.cell.2013.11.039","journal-title":"Cell"},{"issue":"6","key":"371_CR154","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1038\/ni.2607","volume":"14","author":"JS Kim","year":"2013","unstructured":"Kim JS, Sklarz T, Banks LB, Gohil M, Waickman AT, Skuli N, Krock BL, Luo CT, Hu W, Pollizzi KN, Li MO, Rathmell JC, Birnbaum MJ, Powell JD, Jordan MS, Koretzky GA (2013) Natural and inducible TH17 cells are regulated differently by Akt and mTOR pathways. Nat Immunol 14(6):611\u2013618. doi:10.1038\/ni.2607","journal-title":"Nat Immunol"},{"issue":"7295","key":"371_CR155","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1038\/nature09033","volume":"465","author":"TK Kim","year":"2010","unstructured":"Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465(7295):182\u2013187. doi:10.1038\/nature09033","journal-title":"Nature"},{"issue":"5","key":"371_CR156","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1084\/jem.20090313","volume":"206","author":"IL King","year":"2009","unstructured":"King IL, Mohrs M (2009) IL-4-producing CD4+\u00a0T cells in reactive lymph nodes during helminth infection are T follicular helper cells. J Exp Med 206(5):1001\u20131007. doi:10.1084\/jem.20090313","journal-title":"J Exp Med"},{"key":"371_CR157","doi-asserted-by":"publisher","unstructured":"Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP (2010) Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 3 (107):ra8. doi:10.1126\/scisignal.2000568","DOI":"10.1126\/scisignal.2000568"},{"issue":"7446","key":"371_CR158","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1038\/nature11868","volume":"496","author":"M Kleinewietfeld","year":"2013","unstructured":"Kleinewietfeld M, Manzel A, Titze J, Kvakan H, Yosef N, Linker RA, Muller DN, Hafler DA (2013) Sodium chloride drives autoimmune disease by the induction of pathogenic TH17 cells. Nature 496(7446):518\u2013522. doi:10.1038\/nature11868","journal-title":"Nature"},{"issue":"3","key":"371_CR159","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1016\/j.immuni.2012.05.031","volume":"37","author":"MA Koch","year":"2012","unstructured":"Koch MA, Thomas KR, Perdue NR, Smigiel KS, Srivastava S, Campbell DJ (2012) T-bet(+) Treg cells undergo abortive Th1 cell differentiation due to impaired expression of IL-12 receptor beta2. Immunity 37(3):501\u2013510. doi:10.1016\/j.immuni.2012.05.031","journal-title":"Immunity"},{"issue":"6","key":"371_CR160","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/ni.1731","volume":"10","author":"MA Koch","year":"2009","unstructured":"Koch MA, Tucker-Heard G, Perdue NR, Killebrew JR, Urdahl KB, Campbell DJ (2009) The transcription factor T-bet controls regulatory T cell homeostasis and function during type 1 inflammation. Nat Immunol 10(6):595\u2013602","journal-title":"Nat Immunol"},{"issue":"1","key":"371_CR161","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1038\/nm.3432","volume":"20","author":"N Komatsu","year":"2014","unstructured":"Komatsu N, Okamoto K, Sawa S, Nakashima T, Oh-Hora M, Kodama T, Tanaka S, Bluestone JA, Takayanagi H (2014) Pathogenic conversion of Foxp3(+) T cells into TH17 cells in autoimmune arthritis. Nat Med 20(1):62\u201368. doi:10.1038\/nm.3432","journal-title":"Nat Med"},{"issue":"7152","key":"371_CR162","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/nature05970","volume":"448","author":"T Korn","year":"2007","unstructured":"Korn T, Bettelli E, Gao W, Awasthi A, Jager A, Strom TB, Oukka M, Kuchroo VK (2007) IL-21 initiates an alternative pathway to induce proinflammatory T(H)17 cells. Nature 448(7152):484\u2013487","journal-title":"Nature"},{"key":"371_CR163","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1146\/annurev.immunol.021908.132710","volume":"27","author":"T Korn","year":"2009","unstructured":"Korn T, Bettelli E, Oukka M, Kuchroo VK (2009) IL-17 and Th17 Cells. Annu Rev Immunol 27:485\u2013517. doi:10.1146\/annurev.immunol.021908.132710","journal-title":"Annu Rev Immunol"},{"issue":"27","key":"371_CR164","doi-asserted-by":"publisher","first-page":"11193","DOI":"10.1073\/pnas.1019536108","volume":"108","author":"M Kurowska-Stolarska","year":"2011","unstructured":"Kurowska-Stolarska M, Alivernini S, Ballantine LE, Asquith DL, Millar NL, Gilchrist DS, Reilly J, Ierna M, Fraser AR, Stolarski B, McSharry C, Hueber AJ, Baxter D, Hunter J, Gay S, Liew FY, McInnes IB (2011) MicroRNA-155 as a proinflammatory regulator in clinical and experimental arthritis. Proc Natl Acad Sci USA 108(27):11193\u201311198. doi:10.1073\/pnas.1019536108","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6","key":"371_CR165","doi-asserted-by":"publisher","first-page":"941","DOI":"10.1016\/j.immuni.2009.10.008","volume":"31","author":"H Kwon","year":"2009","unstructured":"Kwon H, Thierry-Mieg D, Thierry-Mieg J, Kim HP, Oh J, Tunyaplin C, Carotta S, Donovan CE, Goldman ML, Tailor P, Ozato K, Levy DE, Nutt SL, Calame K, Leonard WJ (2009) Analysis of interleukin-21-induced Prdm1 gene regulation reveals functional cooperation of STAT3 and IRF4 transcription factors. Immunity 31(6):941\u2013952. doi:10.1016\/j.immuni.2009.10.008","journal-title":"Immunity"},{"issue":"1","key":"371_CR166","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/S0014-5793(00)02235-3","volume":"486","author":"V Lafont","year":"2000","unstructured":"Lafont V, Astoul E, Laurence A, Liautard J, Cantrell D (2000) The T cell antigen receptor activates phosphatidylinositol 3-kinase-regulated serine kinases protein kinase B and ribosomal S6 kinase 1. FEBS Lett 486(1):38\u201342","journal-title":"FEBS Lett"},{"issue":"1","key":"371_CR167","doi-asserted-by":"crossref","first-page":"259","DOI":"10.4049\/jimmunol.182.1.259","volume":"182","author":"G Lal","year":"2009","unstructured":"Lal G, Zhang N, van der Touw W, Ding Y, Ju W, Bottinger EP, Reid SP, Levy DE, Bromberg JS (2009) Epigenetic regulation of Foxp3 expression in regulatory T cells by DNA methylation. J Immunol 182(1):259\u2013273","journal-title":"J Immunol"},{"issue":"2","key":"371_CR168","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1016\/j.immuni.2012.05.027","volume":"37","author":"A Laurence","year":"2012","unstructured":"Laurence A, Amarnath S, Mariotti J, Kim YC, Foley J, Eckhaus M, O\u2019Shea JJ, Fowler DH (2012) STAT3 transcription factor promotes instability of nTreg cells and limits generation of iTreg cells during acute murine graft-versus-host disease. Immunity 37(2):209\u2013222. doi:10.1016\/j.immuni.2012.05.027","journal-title":"Immunity"},{"issue":"5","key":"371_CR169","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1016\/S1074-7613(01)00227-8","volume":"15","author":"PP Lee","year":"2001","unstructured":"Lee PP, Fitzpatrick DR, Beard C, Jessup HK, Lehar S, Makar KW, Perez-Melgosa M, Sweetser MT, Schlissel MS, Nguyen S, Cherry SR, Tsai JH, Tucker SM, Weaver WM, Kelso A, Jaenisch R, Wilson CB (2001) A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity 15(5):763\u2013774","journal-title":"Immunity"},{"issue":"10","key":"371_CR170","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1038\/ni.2416","volume":"13","author":"Y Lee","year":"2012","unstructured":"Lee Y, Awasthi A, Yosef N, Quintana FJ, Xiao S, Peters A, Wu C, Kleinewietfeld M, Kunder S, Hafler DA, Sobel RA, Regev A, Kuchroo VK (2012) Induction and molecular signature of pathogenic TH17 cells. Nat Immunol 13(10):991\u2013999. doi:10.1038\/ni.2416","journal-title":"Nat Immunol"},{"issue":"3","key":"371_CR171","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1016\/j.coi.2009.05.021","volume":"21","author":"YK Lee","year":"2009","unstructured":"Lee YK, Mukasa R, Hatton RD, Weaver CT (2009) Developmental plasticity of Th17 and Treg cells. Curr Opin Immunol 21(3):274\u2013280","journal-title":"Curr Opin Immunol"},{"issue":"1\u201312","key":"371_CR172","doi-asserted-by":"publisher","first-page":"1","DOI":"10.2119\/2006-00005.Dinarello","volume":"11","author":"F Leoni","year":"2005","unstructured":"Leoni F, Fossati G, Lewis EC, Lee JK, Porro G, Pagani P, Modena D, Moras ML, Pozzi P, Reznikov LL, Siegmund B, Fantuzzi G, Dinarello CA, Mascagni P (2005) The histone deacetylase inhibitor ITF2357 reduces production of pro-inflammatory cytokines in vitro and systemic inflammation in vivo. Mol Med 11(1\u201312):1\u201315. doi:10.2119\/2006-00005.Dinarello","journal-title":"Mol Med"},{"issue":"5","key":"371_CR173","doi-asserted-by":"publisher","first-page":"2995","DOI":"10.1073\/pnas.052702999","volume":"99","author":"F Leoni","year":"2002","unstructured":"Leoni F, Zaliani A, Bertolini G, Porro G, Pagani P, Pozzi P, Dona G, Fossati G, Sozzani S, Azam T, Bufler P, Fantuzzi G, Goncharov I, Kim SH, Pomerantz BJ, Reznikov LL, Siegmund B, Dinarello CA, Mascagni P (2002) The antitumor histone deacetylase inhibitor suberoylanilide hydroxamic acid exhibits antiinflammatory properties via suppression of cytokines. Proc Natl Acad Sci USA 99(5):2995\u20133000. doi:10.1073\/pnas.052702999","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"371_CR174","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1016\/j.cell.2006.02.017","volume":"124","author":"RE Ley","year":"2006","unstructured":"Ley RE, Peterson DA, Gordon JI (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124(4):837\u2013848. doi:10.1016\/j.cell.2006.02.017","journal-title":"Cell"},{"issue":"10","key":"371_CR175","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1038\/nm.2963","volume":"18","author":"G Li","year":"2012","unstructured":"Li G, Yu M, Lee WW, Tsang M, Krishnan E, Weyand CM, Goronzy JJ (2012) Decline in miR-181a expression with age impairs T cell receptor sensitivity by increasing DUSP6 activity. Nat Med 18(10):1518\u20131524. doi:10.1038\/nm.2963","journal-title":"Nat Med"},{"issue":"3","key":"371_CR176","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1016\/j.cell.2008.07.025","volume":"134","author":"MO Li","year":"2008","unstructured":"Li MO, Flavell RA (2008) TGF-beta: a master of all T cell trades. Cell 134(3):392\u2013404. doi:10.1016\/j.cell.2008.07.025","journal-title":"Cell"},{"issue":"3","key":"371_CR177","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1016\/j.immuni.2006.07.011","volume":"25","author":"MO Li","year":"2006","unstructured":"Li MO, Sanjabi S, Flavell RA (2006) Transforming growth factor-beta controls development, homeostasis, and tolerance of T cells by regulatory T cell-dependent and -independent mechanisms. Immunity 25(3):455\u2013471. doi:10.1016\/j.immuni.2006.07.011","journal-title":"Immunity"},{"issue":"5","key":"371_CR178","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1016\/j.immuni.2007.03.014","volume":"26","author":"MO Li","year":"2007","unstructured":"Li MO, Wan YY, Flavell RA (2007a) T cell-produced transforming growth factor-beta1 controls T cell tolerance and regulates Th1- and Th17-cell differentiation. Immunity 26(5):579\u2013591. doi:10.1016\/j.immuni.2007.03.014","journal-title":"Immunity"},{"issue":"1","key":"371_CR179","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/j.cell.2007.03.008","volume":"129","author":"QJ Li","year":"2007","unstructured":"Li QJ, Chau J, Ebert PJ, Sylvester G, Min H, Liu G, Braich R, Manoharan M, Soutschek J, Skare P, Klein LO, Davis MM, Chen CZ (2007b) miR-181a is an intrinsic modulator of T cell sensitivity and selection. Cell 129(1):147\u2013161. doi:10.1016\/j.cell.2007.03.008","journal-title":"Cell"},{"issue":"7455","key":"371_CR180","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1038\/nature12210","volume":"498","author":"W Li","year":"2013","unstructured":"Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X, Oh S, Kim HS, Glass CK, Rosenfeld MG (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498(7455):516\u2013520. doi:10.1038\/nature12210","journal-title":"Nature"},{"issue":"6","key":"371_CR181","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/ni.2030","volume":"12","author":"W Liao","year":"2011","unstructured":"Liao W, Lin JX, Wang L, Li P, Leonard WJ (2011) Modulation of cytokine receptors by IL-2 broadly regulates differentiation into helper T cell lineages. Nat Immunol 12(6):551\u2013559. doi:10.1038\/ni.2030","journal-title":"Nat Immunol"},{"issue":"5950","key":"371_CR182","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1126\/science.1181369","volume":"326","author":"E Lieberman-Aiden","year":"2009","unstructured":"Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950):289\u2013293. doi:10.1126\/science.1181369","journal-title":"Science"},{"issue":"7","key":"371_CR183","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1038\/sj.bjp.0707165","volume":"150","author":"HS Lin","year":"2007","unstructured":"Lin HS, Hu CY, Chan HY, Liew YY, Huang HP, Lepescheux L, Bastianelli E, Baron R, Rawadi G, Clement-Lacroix P (2007) Anti-rheumatic activities of histone deacetylase (HDAC) inhibitors in vivo in collagen-induced arthritis in rodents. Br J Pharmacol 150(7):862\u2013872. doi:10.1038\/sj.bjp.0707165","journal-title":"Br J Pharmacol"},{"issue":"9","key":"371_CR184","doi-asserted-by":"publisher","first-page":"1993","DOI":"10.1084\/jem.20081062","volume":"205","author":"A Liston","year":"2008","unstructured":"Liston A, Lu LF, O\u2019Carroll D, Tarakhovsky A, Rudensky AY (2008) Dicer-dependent microRNA pathway safeguards regulatory T cell function. J Exp Med 205(9):1993\u20132004. doi:10.1084\/jem.20081062","journal-title":"J Exp Med"},{"issue":"6","key":"371_CR185","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1084\/jem.20080034","volume":"205","author":"M Lochner","year":"2008","unstructured":"Lochner M, Peduto L, Cherrier M, Sawa S, Langa F, Varona R, Riethmacher D, Si-Tahar M, Di Santo JP, Eberl G (2008) In vivo equilibrium of proinflammatory IL-17+\u00a0and regulatory IL-10+\u00a0Foxp3+\u00a0RORgamma t+\u00a0T cells. J Exp Med 205(6):1381\u20131393","journal-title":"J Exp Med"},{"issue":"12","key":"371_CR186","doi-asserted-by":"publisher","first-page":"1113","DOI":"10.1038\/ng.710","volume":"42","author":"S Loewer","year":"2010","unstructured":"Loewer S, Cabili MN, Guttman M, Loh YH, Thomas K, Park IH, Garber M, Curran M, Onder T, Agarwal S, Manos PD, Datta S, Lander ES, Schlaeger TM, Daley GQ, Rinn JL (2010) Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet 42(12):1113\u20131117. doi:10.1038\/ng.710","journal-title":"Nat Genet"},{"issue":"18","key":"371_CR187","doi-asserted-by":"publisher","first-page":"11808","DOI":"10.1073\/pnas.182425099","volume":"99","author":"M Lohoff","year":"2002","unstructured":"Lohoff M, Mittrucker HW, Prechtl S, Bischof S, Sommer F, Kock S, Ferrick DA, Duncan GS, Gessner A, Mak TW (2002) Dysregulated T helper cell differentiation in the absence of interferon regulatory factor 4. Proc Natl Acad Sci USA 99(18):11808\u201311812. doi:10.1073\/pnas.182425099","journal-title":"Proc Natl Acad Sci USA"},{"issue":"53","key":"371_CR188","doi-asserted-by":"publisher","first-page":"41328","DOI":"10.1074\/jbc.M110.146852","volume":"285","author":"F Louafi","year":"2010","unstructured":"Louafi F, Martinez-Nunez RT, Sanchez-Elsner T (2010) MicroRNA-155 targets SMAD2 and modulates the response of macrophages to transforming growth factor-\u03b2. J Biol Chem 285(53):41328\u201341336. doi:10.1074\/jbc.M110.146852","journal-title":"J Biol Chem"},{"issue":"4","key":"371_CR189","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1016\/j.immuni.2011.07.015","volume":"35","author":"KT Lu","year":"2011","unstructured":"Lu KT, Kanno Y, Cannons JL, Handon R, Bible P, Elkahloun AG, Anderson SM, Wei L, Sun H, O\u2019Shea JJ, Schwartzberg PL (2011) Functional and epigenetic studies reveal multistep differentiation and plasticity of in vitro-generated and in vivo-derived follicular T helper cells. Immunity 35(4):622\u2013632. doi:10.1016\/j.immuni.2011.07.015","journal-title":"Immunity"},{"issue":"6","key":"371_CR190","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1016\/j.cell.2010.08.012","volume":"142","author":"LF Lu","year":"2010","unstructured":"Lu LF, Boldin MP, Chaudhry A, Lin LL, Taganov KD, Hanada T, Yoshimura A, Baltimore D, Rudensky AY (2010) Function of miR-146a in controlling Treg cell-mediated regulation of Th1 responses. Cell 142(6):914\u2013929. doi:10.1016\/j.cell.2010.08.012","journal-title":"Cell"},{"issue":"1","key":"371_CR191","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.immuni.2008.11.010","volume":"30","author":"LF Lu","year":"2009","unstructured":"Lu LF, Thai TH, Calado DP, Chaudhry A, Kubo M, Tanaka K, Loeb GB, Lee H, Yoshimura A, Rajewsky K, Rudensky AY (2009) Foxp3-dependent microRNA155 confers competitive fitness to regulatory T cells by targeting SOCS1 protein. Immunity 30(1):80\u201391. doi:10.1016\/j.immuni.2008.11.010","journal-title":"Immunity"},{"issue":"17","key":"371_CR192","doi-asserted-by":"publisher","first-page":"3997","DOI":"10.1182\/blood-2011-11-392985","volume":"119","author":"CS Ma","year":"2012","unstructured":"Ma CS, Avery DT, Chan A, Batten M, Bustamante J, Boisson-Dupuis S, Arkwright PD, Kreins AY, Averbuch D, Engelhard D, Magdorf K, Kilic SS, Minegishi Y, Nonoyama S, French MA, Choo S, Smart JM, Peake J, Wong M, Gray P, Cook MC, Fulcher DA, Casanova JL, Deenick EK, Tangye SG (2012) Functional STAT3 deficiency compromises the generation of human T follicular helper cells. Blood 119(17):3997\u20134008. doi:10.1182\/blood-2011-11-392985","journal-title":"Blood"},{"issue":"4","key":"371_CR193","doi-asserted-by":"publisher","first-page":"e62","DOI":"10.1371\/journal.pgen.0020062","volume":"2","author":"N Maeda","year":"2006","unstructured":"Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engstrom PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, Itoh M, Kanamori-Katayama M, Katayama S, Katoh M, Kawashima T, Quackenbush J, Ravasi T, Ring BZ, Shibata K, Sugiura K, Takenaka Y, Teasdale RD, Wells CA, Zhu Y, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y (2006) Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet 2(4):e62. doi:10.1371\/journal.pgen.0020062","journal-title":"PLoS Genet"},{"issue":"6","key":"371_CR194","doi-asserted-by":"publisher","first-page":"1652","DOI":"10.1002\/eji.201041120","volume":"41","author":"CF Magnani","year":"2011","unstructured":"Magnani CF, Alberigo G, Bacchetta R, Serafini G, Andreani M, Roncarolo MG, Gregori S (2011) Killing of myeloid APCs via HLA class I, CD2 and CD226 defines a novel mechanism of suppression by human Tr1 cells. Eur J Immunol 41(6):1652\u20131662. doi:10.1002\/eji.201041120","journal-title":"Eur J Immunol"},{"issue":"12","key":"371_CR195","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1038\/ni1004","volume":"4","author":"KW Makar","year":"2003","unstructured":"Makar KW, Perez-Melgosa M, Shnyreva M, Weaver WM, Fitzpatrick DR, Wilson CB (2003) Active recruitment of DNA methyltransferases regulates interleukin 4 in thymocytes and T cells. Nat Immunol 4(12):1183\u20131190. doi:10.1038\/ni1004","journal-title":"Nat Immunol"},{"key":"371_CR196","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1007\/978-1-62703-348-0_3","volume":"997","author":"N Malik","year":"2013","unstructured":"Malik N, Rao MS (2013) A review of the methods for human iPSC derivation. Methods Mol Biol 997:23\u201333. doi:10.1007\/978-1-62703-348-0_3","journal-title":"Methods Mol Biol"},{"issue":"7090","key":"371_CR197","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/nature04754","volume":"441","author":"PR Mangan","year":"2006","unstructured":"Mangan PR, Harrington LE, O\u2019Quinn DB, Helms WS, Bullard DC, Elson CO, Hatton RD, Wahl SM, Schoeb TR, Weaver CT (2006) Transforming growth factor-beta induces development of the T(H)17 lineage. Nature 441(7090):231\u2013234","journal-title":"Nature"},{"issue":"2","key":"371_CR198","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1101\/gad.11.2.156","volume":"11","author":"Y Marahrens","year":"1997","unstructured":"Marahrens Y, Panning B, Dausman J, Strauss W, Jaenisch R (1997) Xist-deficient mice are defective in dosage compensation but not spermatogenesis. Genes Dev 11(2):156\u2013166","journal-title":"Genes Dev"},{"issue":"7130","key":"371_CR199","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1038\/nature05478","volume":"445","author":"A Marson","year":"2007","unstructured":"Marson A, Kretschmer K, Frampton GM, Jacobsen ES, Polansky JK, MacIsaac KD, Levine SS, Fraenkel E, von Boehmer H, Young RA (2007) Foxp3 occupancy and regulation of key target genes during T-cell stimulation. Nature 445(7130):931\u2013935. doi:10.1038\/nature05478","journal-title":"Nature"},{"issue":"1","key":"371_CR200","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1002\/bies.080099","volume":"31","author":"JS Mattick","year":"2009","unstructured":"Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF (2009) RNA regulation of epigenetic processes. Bioessays 31(1):51\u201359. doi:10.1002\/bies.080099","journal-title":"Bioessays"},{"issue":"1","key":"371_CR201","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.cell.2005.05.007","volume":"122","author":"SK Mazmanian","year":"2005","unstructured":"Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL (2005) An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122(1):107\u2013118. doi:10.1016\/j.cell.2005.05.007","journal-title":"Cell"},{"issue":"12","key":"371_CR202","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1038\/ni1539","volume":"8","author":"MJ McGeachy","year":"2007","unstructured":"McGeachy MJ, Bak-Jensen KS, Chen Y, Tato CM, Blumenschein W, McClanahan T, Cua DJ (2007) TGF-beta and IL-6 drive the production of IL-17 and IL-10 by T cells and restrain T(H)-17 cell-mediated pathology. Nat Immunol 8(12):1390\u20131397","journal-title":"Nat Immunol"},{"issue":"4","key":"371_CR203","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/j.immuni.2008.03.001","volume":"28","author":"MJ McGeachy","year":"2008","unstructured":"McGeachy MJ, Cua DJ (2008) Th17 cell differentiation: the long and winding road. Immunity 28(4):445\u2013453","journal-title":"Immunity"},{"issue":"11","key":"371_CR204","doi-asserted-by":"publisher","first-page":"2181","DOI":"10.1084\/jem.20130376","volume":"210","author":"DA Mele","year":"2013","unstructured":"Mele DA, Salmeron A, Ghosh S, Huang HR, Bryant BM, Lora JM (2013) BET bromodomain inhibition suppresses TH17-mediated pathology. J Exp Med 210(11):2181\u20132190. doi:10.1084\/jem.20130376","journal-title":"J Exp Med"},{"issue":"3","key":"371_CR205","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1016\/j.molcel.2012.11.021","volume":"49","author":"CA Melo","year":"2013","unstructured":"Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Leveille N, Kalluri R, de Laat W, Agami R (2013) eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 49(3):524\u2013535. doi:10.1016\/j.molcel.2012.11.021","journal-title":"Mol Cell"},{"issue":"7441","key":"371_CR206","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/nature11928","volume":"495","author":"S Memczak","year":"2013","unstructured":"Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495(7441):333\u2013338. doi:10.1038\/nature11928","journal-title":"Nature"},{"issue":"2","key":"371_CR207","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1016\/j.immuni.2011.12.012","volume":"36","author":"T Miyao","year":"2012","unstructured":"Miyao T, Floess S, Setoguchi R, Luche H, Fehling HJ, Waldmann H, Huehn J, Hori S (2012) Plasticity of Foxp3(+) T cells reflects promiscuous Foxp3 expression in conventional T cells but not reprogramming of regulatory T cells. Immunity 36(2):262\u2013275. doi:10.1016\/j.immuni.2011.12.012","journal-title":"Immunity"},{"key":"371_CR208","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1146\/annurev.iy.07.040189.001045","volume":"7","author":"TR Mosmann","year":"1989","unstructured":"Mosmann TR, Coffman RL (1989) TH1 and TH2 cells: different patterns of lymphokine secretion lead to different functional properties. Annu Rev Immunol 7:145\u2013173","journal-title":"Annu Rev Immunol"},{"issue":"Pt 7","key":"371_CR209","doi-asserted-by":"publisher","first-page":"939","DOI":"10.1242\/jcs.024646","volume":"121","author":"M Mourtada-Maarabouni","year":"2008","unstructured":"Mourtada-Maarabouni M, Hedge VL, Kirkham L, Farzaneh F, Williams GT (2008) Growth arrest in human T-cells is controlled by the non-coding RNA growth-arrest-specific transcript 5 (GAS5). J Cell Sci 121(Pt 7):939\u2013946. doi:10.1242\/jcs.024646","journal-title":"J Cell Sci"},{"issue":"5","key":"371_CR210","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1016\/j.molcel.2013.07.022","volume":"51","author":"K Mousavi","year":"2013","unstructured":"Mousavi K, Zare H, Dell\u2019orso S, Grontved L, Gutierrez-Cruz G, Derfoul A, Hager GL, Sartorelli V (2013) eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell 51(5):606\u2013617. doi:10.1016\/j.molcel.2013.07.022","journal-title":"Mol Cell"},{"issue":"3","key":"371_CR211","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/ni.2523","volume":"14","author":"D Mucida","year":"2013","unstructured":"Mucida D, Husain MM, Muroi S, van Wijk F, Shinnakasu R, Naoe Y, Reis BS, Huang Y, Lambolez F, Docherty M, Attinger A, Shui JW, Kim G, Lena CJ, Sakaguchi S, Miyamoto C, Wang P, Atarashi K, Park Y, Nakayama T, Honda K, Ellmeier W, Kronenberg M, Taniuchi I, Cheroutre H (2013) Transcriptional reprogramming of mature CD4(+) helper T cells generates distinct MHC class II-restricted cytotoxic T lymphocytes. Nat Immunol 14(3):281\u2013289. doi:10.1038\/ni.2523","journal-title":"Nat Immunol"},{"issue":"5835","key":"371_CR212","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1126\/science.1145697","volume":"317","author":"D Mucida","year":"2007","unstructured":"Mucida D, Park Y, Kim G, Turovskaya O, Scott I, Kronenberg M, Cheroutre H (2007) Reciprocal TH17 and regulatory T cell differentiation mediated by retinoic acid. Science 317(5835):256\u2013260. doi:10.1126\/science.1145697","journal-title":"Science"},{"key":"371_CR213","doi-asserted-by":"crossref","unstructured":"Mukasa R, Balasubramani A, Lee YK, Whitley SK, Weaver BT, Shibata Y, Crawford GE, Hatton RD, Weaver CT (2010) Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage. Immunity 32 (5):616\u2013627","DOI":"10.1016\/j.immuni.2010.04.016"},{"issue":"5","key":"371_CR214","doi-asserted-by":"publisher","first-page":"2213","DOI":"10.4049\/jimmunol.1003952","volume":"187","author":"G Murugaiyan","year":"2011","unstructured":"Murugaiyan G, Beynon V, Mittal A, Joller N, Weiner HL (2011) Silencing microRNA-155 ameliorates experimental autoimmune encephalomyelitis. J Immunol 187(5):2213\u20132221. doi:10.4049\/jimmunol.1003952","journal-title":"J Immunol"},{"issue":"6098","key":"371_CR215","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1126\/science.1225152","volume":"337","author":"S Naik","year":"2012","unstructured":"Naik S, Bouladoux N, Wilhelm C, Molloy MJ, Salcedo R, Kastenmuller W, Deming C, Quinones M, Koo L, Conlan S, Spencer S, Hall JA, Dzutsev A, Kong H, Campbell DJ, Trinchieri G, Segre JA, Belkaid Y (2012) Compartmentalized control of skin immunity by resident commensals. Science 337(6098):1115\u20131119. doi:10.1126\/science.1225152","journal-title":"Science"},{"issue":"10","key":"371_CR216","doi-asserted-by":"publisher","first-page":"5077","DOI":"10.4049\/jimmunol.1001560","volume":"187","author":"K Nakagome","year":"2011","unstructured":"Nakagome K, Imamura M, Kawahata K, Harada H, Okunishi K, Matsumoto T, Sasaki O, Tanaka R, Kano MR, Chang H, Hanawa H, Miyazaki J, Yamamoto K, Dohi M (2011) High expression of IL-22 suppresses antigen-induced immune responses and eosinophilic airway inflammation via an IL-10-associated mechanism. J Immunol 187(10):5077\u20135089. doi:10.4049\/jimmunol.1001560","journal-title":"J Immunol"},{"issue":"5","key":"371_CR217","doi-asserted-by":"publisher","first-page":"1284","DOI":"10.1002\/art.23429","volume":"58","author":"T Nakasa","year":"2008","unstructured":"Nakasa T, Miyaki S, Okubo A, Hashimoto M, Nishida K, Ochi M, Asahara H (2008) Expression of microRNA-146 in rheumatoid arthritis synovial tissue. Arthritis Rheum 58(5):1284\u20131292. doi:10.1002\/art.23429","journal-title":"Arthritis Rheum"},{"issue":"6","key":"371_CR218","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1016\/j.immuni.2011.11.012","volume":"35","author":"S Nakayamada","year":"2011","unstructured":"Nakayamada S, Kanno Y, Takahashi H, Jankovic D, Lu KT, Johnson TA, Sun HW, Vahedi G, Hakim O, Handon R, Schwartzberg PL, Hager GL, O\u2019Shea JJ (2011) Early Th1 cell differentiation is marked by a Tfh cell-like transition. Immunity 35(6):919\u2013931. doi:10.1016\/j.immuni.2011.11.012","journal-title":"Immunity"},{"issue":"6","key":"371_CR219","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1016\/j.joca.2007.10.014","volume":"16","author":"Y Nasu","year":"2008","unstructured":"Nasu Y, Nishida K, Miyazawa S, Komiyama T, Kadota Y, Abe N, Yoshida A, Hirohata S, Ohtsuka A, Ozaki T (2008) Trichostatin A, a histone deacetylase inhibitor, suppresses synovial inflammation and subsequent cartilage destruction in a collagen antibody-induced arthritis mouse model. Osteoarthritis Cartilage 16(6):723\u2013732. doi:10.1016\/j.joca.2007.10.014","journal-title":"Osteoarthritis Cartilage"},{"issue":"1","key":"371_CR220","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.immuni.2010.07.006","volume":"33","author":"G Natoli","year":"2010","unstructured":"Natoli G (2010) Maintaining cell identity through global control of genomic organization. Immunity 33(1):12\u201324. doi:10.1016\/j.immuni.2010.07.006","journal-title":"Immunity"},{"issue":"3","key":"371_CR221","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1016\/j.cell.2008.11.044","volume":"136","author":"P Nicklin","year":"2009","unstructured":"Nicklin P, Bergman P, Zhang B, Triantafellow E, Wang H, Nyfeler B, Yang H, Hild M, Kung C, Wilson C, Myer VE, MacKeigan JP, Porter JA, Wang YK, Cantley LC, Finan PM, Murphy LO (2009) Bidirectional transport of amino acids regulates mTOR and autophagy. Cell 136(3):521\u2013534. doi:10.1016\/j.cell.2008.11.044","journal-title":"Cell"},{"key":"371_CR222","doi-asserted-by":"publisher","unstructured":"Nishida K, Komiyama T, Miyazawa S, Shen ZN, Furumatsu T, Doi H, Yoshida A, Yamana J, Yamamura M, Ninomiya Y, Inoue H, Asahara H (2004) Histone deacetylase inhibitor suppression of autoantibody-mediated arthritis in mice via regulation of p16INK4a and p21(WAF1\/Cip1) expression. Arthritis Rheum 50 (10):3365\u20133376. doi:10.1002\/art.20709","DOI":"10.1002\/art.20709"},{"issue":"33","key":"371_CR223","doi-asserted-by":"publisher","first-page":"14751","DOI":"10.1073\/pnas.1003852107","volume":"107","author":"K Nistala","year":"2010","unstructured":"Nistala K, Adams S, Cambrook H, Ursu S, Olivito B, de Jager W, Evans JG, Cimaz R, Bajaj-Elliott M, Wedderburn LR (2010) Th17 plasticity in human autoimmune arthritis is driven by the inflammatory environment. Proc Natl Acad Sci USA 107(33):14751\u201314756. doi:10.1073\/pnas.1003852107","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"371_CR224","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1002\/art.23291","volume":"58","author":"K Nistala","year":"2008","unstructured":"Nistala K, Moncrieffe H, Newton KR, Varsani H, Hunter P, Wedderburn LR (2008) Interleukin-17-producing T cells are enriched in the joints of children with arthritis, but have a reciprocal relationship to regulatory T cell numbers. Arthritis Rheum 58(3):875\u2013887. doi:10.1002\/art.23291","journal-title":"Arthritis Rheum"},{"key":"371_CR225","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1146\/annurev-genom-082509-141651","volume":"11","author":"JP Noonan","year":"2010","unstructured":"Noonan JP, McCallion AS (2010) Genomics of long-range regulatory elements. Annu Rev Genomics Hum Genet 11:1\u201323. doi:10.1146\/annurev-genom-082509-141651","journal-title":"Annu Rev Genomics Hum Genet"},{"issue":"7398","key":"371_CR226","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1038\/nature11049","volume":"485","author":"EP Nora","year":"2012","unstructured":"Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Bluthgen N, Dekker J, Heard E (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485(7398):381\u2013385. doi:10.1038\/nature11049","journal-title":"Nature"},{"issue":"5943","key":"371_CR227","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1126\/science.1176676","volume":"325","author":"RI Nurieva","year":"2009","unstructured":"Nurieva RI, Chung Y, Martinez GJ, Yang XO, Tanaka S, Matskevitch TD, Wang YH, Dong C (2009) Bcl6 mediates the development of T follicular helper cells. Science 325(5943):1001\u20131005. doi:10.1126\/science.1176676","journal-title":"Science"},{"issue":"14","key":"371_CR228","doi-asserted-by":"publisher","first-page":"11234","DOI":"10.1074\/jbc.M111.324046","volume":"287","author":"RI Nurieva","year":"2012","unstructured":"Nurieva RI, Podd A, Chen Y, Alekseev AM, Yu M, Qi X, Huang H, Wen R, Wang J, Li HS, Watowich SS, Qi H, Dong C, Wang D (2012) STAT5 protein negatively regulates T follicular helper (Tfh) cell generation and function. J Biol Chem 287(14):11234\u201311239. doi:10.1074\/jbc.M111.324046","journal-title":"J Biol Chem"},{"issue":"4","key":"371_CR229","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/j.immuni.2010.09.009","volume":"33","author":"RM O\u2019Connell","year":"2010","unstructured":"O\u2019Connell RM, Kahn D, Gibson WS, Round JL, Scholz RL, Chaudhuri AA, Kahn ME, Rao DS, Baltimore D (2010a) MicroRNA-155 promotes autoimmune inflammation by enhancing inflammatory T cell development. Immunity 33(4):607\u2013619. doi:10.1016\/j.immuni.2010.09.009","journal-title":"Immunity"},{"issue":"2","key":"371_CR230","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1038\/nri2708","volume":"10","author":"RM O\u2019Connell","year":"2010","unstructured":"O\u2019Connell RM, Rao DS, Chaudhuri AA, Baltimore D (2010b) Physiological and pathological roles for microRNAs in the immune system. Nat Rev Immunol 10(2):111\u2013122. doi:10.1038\/nri2708","journal-title":"Nat Rev Immunol"},{"issue":"5969","key":"371_CR232","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.1126\/science.1178334","volume":"327","author":"JJ O\u2019Shea","year":"2010","unstructured":"O\u2019Shea JJ, Paul WE (2010) Mechanisms underlying lineage commitment and plasticity of helper CD4+\u00a0T cells. Science 327(5969):1098\u20131102. doi:10.1126\/science.1178334","journal-title":"Science"},{"issue":"7485","key":"371_CR233","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1038\/nature12968","volume":"505","author":"H Obokata","year":"2014","unstructured":"Obokata H, Wakayama T, Sasai Y, Kojima K, Vacanti MP, Niwa H, Yamato M, Vacanti CA (2014) Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature 505(7485):641\u2013647. doi:10.1038\/nature12968","journal-title":"Nature"},{"issue":"5","key":"371_CR234","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1084\/jem.20102144","volume":"208","author":"KJ Oestreich","year":"2011","unstructured":"Oestreich KJ, Huang AC, Weinmann AS (2011) The lineage-defining factors T-bet and Bcl-6 collaborate to regulate Th1 gene expression patterns. J Exp Med 208(5):1001\u20131013. doi:10.1084\/jem.20102144","journal-title":"J Exp Med"},{"issue":"4","key":"371_CR235","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1038\/ni.2242","volume":"13","author":"KJ Oestreich","year":"2012","unstructured":"Oestreich KJ, Mohn SE, Weinmann AS (2012) Molecular mechanisms that control the expression and activity of Bcl-6 in TH1 cells to regulate flexibility with a TFH-like gene profile. Nat Immunol 13(4):405\u2013411. doi:10.1038\/ni.2242","journal-title":"Nat Immunol"},{"issue":"8","key":"371_CR236","doi-asserted-by":"publisher","first-page":"3973","DOI":"10.4049\/jimmunol.1301843","volume":"191","author":"SA Oh","year":"2013","unstructured":"Oh SA, Li MO (2013) TGF-beta: guardian of T cell function. J Immunol 191(8):3973\u20133979. doi:10.4049\/jimmunol.1301843","journal-title":"J Immunol"},{"issue":"5","key":"371_CR237","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1016\/j.immuni.2012.09.010","volume":"37","author":"N Ohkura","year":"2012","unstructured":"Ohkura N, Hamaguchi M, Morikawa H, Sugimura K, Tanaka A, Ito Y, Osaki M, Tanaka Y, Yamashita R, Nakano N, Huehn J, Fehling HJ, Sparwasser T, Nakai K, Sakaguchi S (2012) T cell receptor stimulation-induced epigenetic changes and Foxp3 expression are independent and complementary events required for Treg cell development. Immunity 37(5):785\u2013799. doi:10.1016\/j.immuni.2012.09.010","journal-title":"Immunity"},{"issue":"3","key":"371_CR238","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1016\/j.immuni.2013.03.002","volume":"38","author":"N Ohkura","year":"2013","unstructured":"Ohkura N, Kitagawa Y, Sakaguchi S (2013) Development and maintenance of regulatory T cells. Immunity 38(3):414\u2013423. doi:10.1016\/j.immuni.2013.03.002","journal-title":"Immunity"},{"issue":"3","key":"371_CR239","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/S0092-8674(00)81656-6","volume":"99","author":"M Okano","year":"1999","unstructured":"Okano M, Bell DW, Haber DA, Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99(3):247\u2013257","journal-title":"Cell"},{"issue":"3","key":"371_CR240","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1038\/890","volume":"19","author":"M Okano","year":"1998","unstructured":"Okano M, Xie S, Li E (1998) Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat Genet 19(3):219\u2013220. doi:10.1038\/890","journal-title":"Nat Genet"},{"issue":"5","key":"371_CR241","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1016\/j.immuni.2009.10.001","volume":"31","author":"G Oldenhove","year":"2009","unstructured":"Oldenhove G, Bouladoux N, Wohlfert EA, Hall JA, Chou D, Dos Santos L, O\u2019Brien S, Blank R, Lamb E, Natarajan S, Kastenmayer R, Hunter C, Grigg ME, Belkaid Y (2009) Decrease of Foxp3+\u00a0Treg cell number and acquisition of effector cell phenotype during lethal infection. Immunity 31(5):772\u2013786. doi:10.1016\/j.immuni.2009.10.001","journal-title":"Immunity"},{"issue":"6","key":"371_CR242","doi-asserted-by":"publisher","first-page":"2682","DOI":"10.4049\/jimmunol.1202534","volume":"190","author":"AC Palin","year":"2013","unstructured":"Palin AC, Ramachandran V, Acharya S, Lewis DB (2013) Human neonatal naive CD4+\u00a0T cells have enhanced activation-dependent signaling regulated by the microRNA miR-181a. J Immunol 190(6):2682\u20132691. doi:10.4049\/jimmunol.1202534","journal-title":"J Immunol"},{"issue":"12","key":"371_CR243","doi-asserted-by":"publisher","first-page":"7738","DOI":"10.4049\/jimmunol.0900603","volume":"182","author":"KC Pang","year":"2009","unstructured":"Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, Mattick JS (2009) Genome-wide identification of long noncoding RNAs in CD8+\u00a0T cells. J Immunol 182(12):7738\u20137748. doi:10.4049\/jimmunol.0900603","journal-title":"J Immunol"},{"issue":"4","key":"371_CR244","doi-asserted-by":"publisher","first-page":"R101","DOI":"10.1186\/ar2493","volume":"10","author":"KM Pauley","year":"2008","unstructured":"Pauley KM, Satoh M, Chan AL, Bubb MR, Reeves WH, Chan EK (2008) Upregulated miR-146a expression in peripheral blood mononuclear cells from rheumatoid arthritis patients. Arthritis Res Ther 10(4):R101. doi:10.1186\/ar2493","journal-title":"Arthritis Res Ther"},{"issue":"8","key":"371_CR245","doi-asserted-by":"publisher","first-page":"e1001633","DOI":"10.1371\/journal.pbio.1001633","volume":"11","author":"M Peine","year":"2013","unstructured":"Peine M, Rausch S, Helmstetter C, Frohlich A, Hegazy AN, Kuhl AA, Grevelding CG, Hofer T, Hartmann S, Lohning M (2013) Stable T-bet(+)GATA-3(+) Th1\/Th2 hybrid cells arise in vivo, can develop directly from naive precursors, and limit immunopathologic inflammation. PLoS Biol 11(8):e1001633. doi:10.1371\/journal.pbio.1001633","journal-title":"PLoS Biol"},{"issue":"6","key":"371_CR246","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1016\/j.cell.2013.04.053","volume":"153","author":"JE Phillips-Cremins","year":"2013","unstructured":"Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, Bland MJ, Wagstaff W, Dalton S, McDevitt TC, Sen R, Dekker J, Taylor J, Corces VG (2013) Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153(6):1281\u20131295. doi:10.1016\/j.cell.2013.04.053","journal-title":"Cell"},{"issue":"1","key":"371_CR247","doi-asserted-by":"publisher","first-page":"313","DOI":"10.4049\/jimmunol.0904023","volume":"185","author":"AC Poholek","year":"2010","unstructured":"Poholek AC, Hansen K, Hernandez SG, Eto D, Chandele A, Weinstein JS, Dong X, Odegard JM, Kaech SM, Dent AL, Crotty S, Craft J (2010) In vivo regulation of Bcl6 and T follicular helper cell development. J Immunol 185(1):313\u2013326. doi:10.4049\/jimmunol.0904023","journal-title":"J Immunol"},{"issue":"6","key":"371_CR248","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1002\/eji.200838105","volume":"38","author":"JK Polansky","year":"2008","unstructured":"Polansky JK, Kretschmer K, Freyer J, Floess S, Garbe A, Baron U, Olek S, Hamann A, von Boehmer H, Huehn J (2008) DNA methylation controls Foxp3 gene expression. Eur J Immunol 38(6):1654\u20131663","journal-title":"Eur J Immunol"},{"issue":"7301","key":"371_CR249","doi-asserted-by":"publisher","first-page":"1033","DOI":"10.1038\/nature09144","volume":"465","author":"L Poliseno","year":"2010","unstructured":"Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465(7301):1033\u20131038. doi:10.1038\/nature09144","journal-title":"Nature"},{"issue":"2","key":"371_CR250","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1111\/j.1574-6968.2002.tb11467.x","volume":"217","author":"SE Pryde","year":"2002","unstructured":"Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ (2002) The microbiology of butyrate formation in the human colon. FEMS Microbiol Lett 217(2):133\u2013139","journal-title":"FEMS Microbiol Lett"},{"issue":"1","key":"371_CR251","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1172\/JCI116576","volume":"92","author":"J Quddus","year":"1993","unstructured":"Quddus J, Johnson KJ, Gavalchin J, Amento EP, Chrisp CE, Yung RL, Richardson BC (1993) Treating activated CD4+\u00a0T cells with either of two distinct DNA methyltransferase inhibitors, 5-azacytidine or procainamide, is sufficient to cause a lupus-like disease in syngeneic mice. J Clin Investig 92(1):38\u201353. doi:10.1172\/JCI116576","journal-title":"J Clin Investig"},{"issue":"6","key":"371_CR252","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841\u2013842. doi:10.1093\/bioinformatics\/btq033","journal-title":"Bioinformatics"},{"issue":"7","key":"371_CR253","doi-asserted-by":"publisher","first-page":"3111","DOI":"10.1073\/pnas.0910667107","volume":"107","author":"D Rai","year":"2010","unstructured":"Rai D, Kim SW, McKeller MR, Dahia PL, Aguiar RC (2010) Targeting of SMAD5 links microRNA-155 to the TGF-beta pathway and lymphomagenesis. Proc Natl Acad Sci USA 107(7):3111\u20133116. doi:10.1073\/pnas.0910667107","journal-title":"Proc Natl Acad Sci USA"},{"issue":"5838","key":"371_CR254","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1126\/science.1143775","volume":"317","author":"SL Reiner","year":"2007","unstructured":"Reiner SL, Sallusto F, Lanzavecchia A (2007) Division of labor with a workforce of one: challenges in specifying effector and memory T cell fate. Science 317(5838):622\u2013625","journal-title":"Science"},{"issue":"4","key":"371_CR255","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1038\/ni.1715","volume":"10","author":"RL Reinhardt","year":"2009","unstructured":"Reinhardt RL, Liang HE, Locksley RM (2009) Cytokine-secreting follicular T cells shape the antibody repertoire. Nat Immunol 10(4):385\u2013393. doi:10.1038\/ni.1715","journal-title":"Nat Immunol"},{"issue":"11","key":"371_CR256","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1002\/art.1780331109","volume":"33","author":"B Richardson","year":"1990","unstructured":"Richardson B, Scheinbart L, Strahler J, Gross L, Hanash S, Johnson M (1990) Evidence for impaired T cell DNA methylation in systemic lupus erythematosus and rheumatoid arthritis. Arthritis Rheum 33(11):1665\u20131673","journal-title":"Arthritis Rheum"},{"issue":"1","key":"371_CR257","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.cell.2013.09.011","volume":"155","author":"CM Rivera","year":"2013","unstructured":"Rivera CM, Ren B (2013) Mapping human epigenomes. Cell 155(1):39\u201355. doi:10.1016\/j.cell.2013.09.011","journal-title":"Cell"},{"issue":"11","key":"371_CR258","doi-asserted-by":"publisher","first-page":"e1182","DOI":"10.1371\/journal.pone.0001182","volume":"2","author":"A Rodriguez-Campos","year":"2007","unstructured":"Rodriguez-Campos A, Azorin F (2007) RNA is an integral component of chromatin that contributes to its structural organization. PLoS ONE 2(11):e1182. doi:10.1371\/journal.pone.0001182","journal-title":"PLoS ONE"},{"issue":"5824","key":"371_CR259","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1126\/science.1139253","volume":"316","author":"A Rodriguez","year":"2007","unstructured":"Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P, Soond DR, van Dongen S, Grocock RJ, Das PP, Miska EA, Vetrie D, Okkenhaug K, Enright AJ, Dougan G, Turner M, Bradley A (2007) Requirement of bic\/microRNA-155 for normal immune function. Science 316(5824):608\u2013611. doi:10.1126\/science.1139253","journal-title":"Science"},{"issue":"6","key":"371_CR260","doi-asserted-by":"publisher","first-page":"1681","DOI":"10.1002\/eji.200526189","volume":"35","author":"G Roncador","year":"2005","unstructured":"Roncador G, Brown PJ, Maestre L, Hue S, Martinez-Torrecuadrada JL, Ling KL, Pratap S, Toms C, Fox BC, Cerundolo V, Powrie F, Banham AH (2005) Analysis of FOXP3 protein expression in human CD4+\u00a0CD25+\u00a0regulatory T cells at the single-cell level. Eur J Immunol 35(6):1681\u20131691. doi:10.1002\/eji.200526189","journal-title":"Eur J Immunol"},{"issue":"27","key":"371_CR261","doi-asserted-by":"publisher","first-page":"12204","DOI":"10.1073\/pnas.0909122107","volume":"107","author":"JL Round","year":"2010","unstructured":"Round JL, Mazmanian SK (2010) Inducible Foxp3+\u00a0regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci USA 107(27):12204\u201312209. doi:10.1073\/pnas.0909122107","journal-title":"Proc Natl Acad Sci USA"},{"issue":"5999","key":"371_CR262","doi-asserted-by":"publisher","first-page":"1667","DOI":"10.1126\/science.1191996","volume":"329","author":"YP Rubtsov","year":"2010","unstructured":"Rubtsov YP, Niec RE, Josefowicz S, Li L, Darce J, Mathis D, Benoist C, Rudensky AY (2010) Stability of the regulatory T cell lineage in vivo. Science 329(5999):1667\u20131671. doi:10.1126\/science.1191996","journal-title":"Science"},{"issue":"1","key":"371_CR263","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1111\/j.1600-065X.2011.01018.x","volume":"241","author":"AY Rudensky","year":"2011","unstructured":"Rudensky AY (2011) Regulatory T cells and Foxp3. Immunol Rev 241(1):260\u2013268. doi:10.1111\/j.1600-065X.2011.01018.x","journal-title":"Immunol Rev"},{"issue":"5","key":"371_CR264","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1016\/j.cell.2008.05.009","volume":"133","author":"S Sakaguchi","year":"2008","unstructured":"Sakaguchi S, Yamaguchi T, Nomura T, Ono M (2008) Regulatory T cells and immune tolerance. Cell 133(5):775\u2013787. doi:10.1016\/j.cell.2008.05.009","journal-title":"Cell"},{"issue":"3","key":"371_CR265","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1016\/j.cell.2011.07.014","volume":"146","author":"L Salmena","year":"2011","unstructured":"Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146(3):353\u2013358. doi:10.1016\/j.cell.2011.07.014","journal-title":"Cell"},{"issue":"1","key":"371_CR266","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/j.cell.2012.06.053","volume":"151","author":"RM Samstein","year":"2012","unstructured":"Samstein RM, Arvey A, Josefowicz SZ, Peng X, Reynolds A, Sandstrom R, Neph S, Sabo P, Kim JM, Liao W, Li MO, Leslie C, Stamatoyannopoulos JA, Rudensky AY (2012) Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Cell 151(1):153\u2013166. doi:10.1016\/j.cell.2012.06.053","journal-title":"Cell"},{"issue":"4","key":"371_CR267","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1007\/s10577-009-9040-3","volume":"17","author":"S Santangelo","year":"2009","unstructured":"Santangelo S, Cousins DJ, Winkelmann N, Triantaphyllopoulos K, Staynov DZ (2009) Chromatin structure and DNA methylation of the IL-4 gene in human T(H)2 cells. Chromosome Res 17(4):485\u2013496. doi:10.1007\/s10577-009-9040-3","journal-title":"Chromosome Res"},{"issue":"2","key":"371_CR268","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.yexmp.2009.06.003","volume":"87","author":"SJ Saouaf","year":"2009","unstructured":"Saouaf SJ, Li B, Zhang G, Shen Y, Furuuchi N, Hancock WW, Greene MI (2009) Deacetylase inhibition increases regulatory T cell function and decreases incidence and severity of collagen-induced arthritis. Exp Mol Pathol 87(2):99\u2013104. doi:10.1016\/j.yexmp.2009.06.003","journal-title":"Exp Mol Pathol"},{"key":"371_CR269","doi-asserted-by":"publisher","first-page":"e01749","DOI":"10.7554\/eLife.01749","volume":"2","author":"M Sauvageau","year":"2013","unstructured":"Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, Liapis SC, Mallard W, Morse M, Swerdel MR, D\u2019Ecclessis MF, Moore JC, Lai V, Gong G, Yancopoulos GD, Frendewey D, Kellis M, Hart RP, Valenzuela DM, Arlotta P, Rinn JL (2013) Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife 2:e01749. doi:10.7554\/eLife.01749","journal-title":"Elife"},{"issue":"12","key":"371_CR270","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1084\/jem.20050419","volume":"201","author":"B Sawitzki","year":"2005","unstructured":"Sawitzki B, Kingsley CI, Oliveira V, Karim M, Herber M, Wood KJ (2005) IFN-gamma production by alloantigen-reactive regulatory T cells is important for their regulatory function in vivo. J Exp Med 201(12):1925\u20131935. doi:10.1084\/jem.20050419","journal-title":"J Exp Med"},{"issue":"5","key":"371_CR271","doi-asserted-by":"publisher","first-page":"1491","DOI":"10.1002\/eji.201041067","volume":"41","author":"C Schmidl","year":"2011","unstructured":"Schmidl C, Hansmann L, Andreesen R, Edinger M, Hoffmann P, Rehli M (2011) Epigenetic reprogramming of the RORC locus during in vitro expansion is a distinctive feature of human memory but not naive Treg. Eur J Immunol 41(5):1491\u20131498. doi:10.1002\/eji.201041067","journal-title":"Eur J Immunol"},{"issue":"17","key":"371_CR272","doi-asserted-by":"publisher","first-page":"3375","DOI":"10.1182\/blood-2012-08-448902","volume":"121","author":"N Schmitt","year":"2013","unstructured":"Schmitt N, Bustamante J, Bourdery L, Bentebibel SE, Boisson-Dupuis S, Hamlin F, Tran MV, Blankenship D, Pascual V, Savino DA, Banchereau J, Casanova JL, Ueno H (2013) IL-12 receptor beta1 deficiency alters in vivo T follicular helper cell response in humans. Blood 121(17):3375\u20133385. doi:10.1182\/blood-2012-08-448902","journal-title":"Blood"},{"issue":"6","key":"371_CR273","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/S0092-8674(88)91065-3","volume":"54","author":"C Schneider","year":"1988","unstructured":"Schneider C, King RM, Philipson L (1988) Genes specifically expressed at growth arrest of mammalian cells. Cell 54(6):787\u2013793","journal-title":"Cell"},{"issue":"7","key":"371_CR274","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1038\/ni1474","volume":"8","author":"JR Schoenborn","year":"2007","unstructured":"Schoenborn JR, Dorschner MO, Sekimata M, Santer DM, Shnyreva M, Fitzpatrick DR, Stamatoyannopoulos JA, Wilson CB (2007) Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing transcription of the gene encoding interferon-gamma. Nat Immunol 8(7):732\u2013742","journal-title":"Nat Immunol"},{"issue":"4","key":"371_CR275","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1016\/j.immuni.2009.08.021","volume":"31","author":"M Sekimata","year":"2009","unstructured":"Sekimata M, Perez-Melgosa M, Miller SA, Weinmann AS, Sabo PJ, Sandstrom R, Dorschner MO, Stamatoyannopoulos JA, Wilson CB (2009) CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus. Immunity 31(4):551\u2013564. doi:10.1016\/j.immuni.2009.08.021","journal-title":"Immunity"},{"issue":"5","key":"371_CR276","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1016\/j.immuni.2013.01.013","volume":"38","author":"MD Sharma","year":"2013","unstructured":"Sharma MD, Huang L, Choi JH, Lee EJ, Wilson JM, Lemos H, Pan F, Blazar BR, Pardoll DM, Mellor AL, Shi H, Munn DH (2013) An inherently bifunctional subset of Foxp3+\u00a0T helper cells is controlled by the transcription factor eos. Immunity 38(5):998\u20131012. doi:10.1016\/j.immuni.2013.01.013","journal-title":"Immunity"},{"issue":"28","key":"371_CR277","doi-asserted-by":"publisher","first-page":"11381","DOI":"10.1073\/pnas.1019711108","volume":"108","author":"S Sharma","year":"2011","unstructured":"Sharma S, Findlay GM, Bandukwala HS, Oberdoerffer S, Baust B, Li Z, Schmidt V, Hogan PG, Sacks DB, Rao A (2011) Dephosphorylation of the nuclear factor of activated T cells (NFAT) transcription factor is regulated by an RNA-protein scaffold complex. Proc Natl Acad Sci USA 108(28):11381\u201311386. doi:10.1073\/pnas.1019711108","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"371_CR278","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1261\/rna.1441510","volume":"16","author":"J Sheik Mohamed","year":"2010","unstructured":"Sheik Mohamed J, Gaughwin PM, Lim B, Robson P, Lipovich L (2010) Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA 16(2):324\u2013337. doi:10.1261\/rna.1441510","journal-title":"RNA"},{"key":"371_CR279","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1146\/annurev.immunol.18.1.423","volume":"18","author":"EM Shevach","year":"2000","unstructured":"Shevach EM (2000) Regulatory T cells in autoimmmunity*. Annu Rev Immunol 18:423\u2013449","journal-title":"Annu Rev Immunol"},{"issue":"2","key":"371_CR280","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/j.smim.2006.10.002","volume":"19","author":"K Smith","year":"2007","unstructured":"Smith K, McCoy KD, Macpherson AJ (2007) Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin Immunol 19(2):59\u201369. doi:10.1016\/j.smim.2006.10.002","journal-title":"Semin Immunol"},{"issue":"6145","key":"371_CR281","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1126\/science.1241165","volume":"341","author":"PM Smith","year":"2013","unstructured":"Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly YM, Glickman JN, Garrett WS (2013) The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341(6145):569\u2013573. doi:10.1126\/science.1241165","journal-title":"Science"},{"key":"371_CR282","doi-asserted-by":"publisher","unstructured":"Sonkoly E, Janson P, Majuri ML, Savinko T, Fyhrquist N, Eidsmo L, Xu N, Meisgen F, Wei T, Bradley M, Stenvang J, Kauppinen S, Alenius H, Lauerma A, Homey B, Winqvist O, Stahle M, Pivarcsi A (2010) MiR-155 is overexpressed in patients with atopic dermatitis and modulates T-cell proliferative responses by targeting cytotoxic T lymphocyte-associated antigen 4. J Allergy Clin Immunol 126 (3):581\u2013589 e581\u2013520. doi:10.1016\/j.jaci.2010.05.045","DOI":"10.1016\/j.jaci.2010.05.045"},{"issue":"10","key":"371_CR283","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1038\/ni1115","volume":"5","author":"CG Spilianakis","year":"2004","unstructured":"Spilianakis CG, Flavell RA (2004) Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol 5(10):1017\u20131027. doi:10.1038\/ni1115","journal-title":"Nat Immunol"},{"issue":"7042","key":"371_CR284","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1038\/nature03574","volume":"435","author":"CG Spilianakis","year":"2005","unstructured":"Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA (2005) Interchromosomal associations between alternatively expressed loci. Nature 435(7042):637\u2013645. doi:10.1038\/nature03574","journal-title":"Nature"},{"issue":"2","key":"371_CR285","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1016\/j.immuni.2010.07.014","volume":"33","author":"V Staudt","year":"2010","unstructured":"Staudt V, Bothur E, Klein M, Lingnau K, Reuter S, Grebe N, Gerlitzki B, Hoffmann M, Ulges A, Taube C, Dehzad N, Becker M, Stassen M, Steinborn A, Lohoff M, Schild H, Schmitt E, Bopp T (2010) Interferon-regulatory factor 4 is essential for the developmental program of T helper 9 cells. Immunity 33(2):192\u2013202. doi:10.1016\/j.immuni.2010.07.014","journal-title":"Immunity"},{"issue":"2","key":"371_CR286","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1038\/nm1551","volume":"13","author":"L Steinman","year":"2007","unstructured":"Steinman L (2007) A brief history of T(H)17, the first major revision in the T(H)1\/T(H)2 hypothesis of T cell-mediated tissue damage. Nat Med 13(2):139\u2013145. doi:10.1038\/nm1551","journal-title":"Nat Med"},{"issue":"11","key":"371_CR287","doi-asserted-by":"publisher","first-page":"1149","DOI":"10.1038\/ni1122","volume":"5","author":"P Stock","year":"2004","unstructured":"Stock P, Akbari O, Berry G, Freeman GJ, Dekruyff RH, Umetsu DT (2004) Induction of T helper type 1-like regulatory cells that express Foxp3 and protect against airway hyper-reactivity. Nat Immunol 5(11):1149\u20131156. doi:10.1038\/ni1122","journal-title":"Nat Immunol"},{"issue":"6","key":"371_CR288","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1016\/j.smim.2007.10.008","volume":"19","author":"B Stockinger","year":"2007","unstructured":"Stockinger B, Veldhoen M, Martin B (2007) Th17 T cells: linking innate and adaptive immunity. Semin Immunol 19(6):353\u2013361. doi:10.1016\/j.smim.2007.10.008","journal-title":"Semin Immunol"},{"issue":"5","key":"371_CR289","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1084\/jem.185.5.817","volume":"185","author":"SJ Szabo","year":"1997","unstructured":"Szabo SJ, Dighe AS, Gubler U, Murphy KM (1997) Regulation of the interleukin (IL)-12R beta 2 subunit expression in developing T helper 1 (Th1) and Th2 cells. J Exp Med 185(5):817\u2013824","journal-title":"J Exp Med"},{"issue":"6","key":"371_CR290","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1016\/S0092-8674(00)80702-3","volume":"100","author":"SJ Szabo","year":"2000","unstructured":"Szabo SJ, Kim ST, Costa GL, Zhang X, Fathman CG, Glimcher LH (2000) A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell 100(6):655\u2013669","journal-title":"Cell"},{"issue":"6","key":"371_CR291","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/ni.2286","volume":"13","author":"H Takahashi","year":"2012","unstructured":"Takahashi H, Kanno T, Nakayamada S, Hirahara K, Sciume G, Muljo SA, Kuchen S, Casellas R, Wei L, Kanno Y, O\u2019Shea JJ (2012) TGF-beta and retinoic acid induce the microRNA miR-10a, which targets Bcl-6 and constrains the plasticity of helper T cells. Nat Immunol 13(6):587\u2013595. doi:10.1038\/ni.2286","journal-title":"Nat Immunol"},{"issue":"4","key":"371_CR292","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1002\/art.24436","volume":"60","author":"Y Tang","year":"2009","unstructured":"Tang Y, Luo X, Cui H, Ni X, Yuan M, Guo Y, Huang X, Zhou H, de Vries N, Tak PP, Chen S, Shen N (2009) MicroRNA-146A contributes to abnormal activation of the type I interferon pathway in human lupus by targeting the key signaling proteins. Arthritis Rheum 60(4):1065\u20131075. doi:10.1002\/art.24436","journal-title":"Arthritis Rheum"},{"issue":"27","key":"371_CR293","doi-asserted-by":"publisher","first-page":"22900","DOI":"10.1074\/jbc.M111.312785","volume":"287","author":"RM Thomas","year":"2012","unstructured":"Thomas RM, Gamper CJ, Ladle BH, Powell JD, Wells AD (2012) De novo DNA methylation is required to restrict T helper lineage plasticity. J Biol Chem 287(27):22900\u201322909. doi:10.1074\/jbc.M111.312785","journal-title":"J Biol Chem"},{"issue":"7","key":"371_CR294","doi-asserted-by":"publisher","first-page":"3433","DOI":"10.4049\/jimmunol.0904028","volume":"184","author":"AM Thornton","year":"2010","unstructured":"Thornton AM, Korty PE, Tran DQ, Wohlfert EA, Murray PE, Belkaid Y, Shevach EM (2010) Expression of Helios, an Ikaros transcription factor family member, differentiates thymic-derived from peripherally induced Foxp3+\u00a0T regulatory cells. J Immunol 184(7):3433\u20133441. doi:10.4049\/jimmunol.0904028","journal-title":"J Immunol"},{"issue":"8","key":"371_CR295","doi-asserted-by":"publisher","first-page":"864","DOI":"10.1038\/ni.1770","volume":"10","author":"S Trifari","year":"2009","unstructured":"Trifari S, Kaplan CD, Tran EH, Crellin NK, Spits H (2009) Identification of a human helper T cell population that has abundant production of interleukin 22 and is distinct from T(H)-17, T(H)1 and T(H)2 cells. Nat Immunol 10(8):864\u2013871. doi:10.1038\/ni.1770","journal-title":"Nat Immunol"},{"issue":"5","key":"371_CR296","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1016\/j.immuni.2013.09.012","volume":"39","author":"DJ Tumes","year":"2013","unstructured":"Tumes DJ, Onodera A, Suzuki A, Shinoda K, Endo Y, Iwamura C, Hosokawa H, Koseki H, Tokoyoda K, Suzuki Y, Motohashi S, Nakayama T (2013) The polycomb protein Ezh2 regulates differentiation and plasticity of CD4(+) T helper type 1 and type 2 cells. Immunity 39(5):819\u2013832. doi:10.1016\/j.immuni.2013.09.012","journal-title":"Immunity"},{"issue":"7","key":"371_CR297","doi-asserted-by":"crossref","first-page":"3504","DOI":"10.1128\/IAI.67.7.3504-3511.1999","volume":"67","author":"Y Umesaki","year":"1999","unstructured":"Umesaki Y, Setoyama H, Matsumoto S, Imaoka A, Itoh K (1999) Differential roles of segmented filamentous bacteria and clostridia in development of the intestinal immune system. Infect Immun 67(7):3504\u20133511","journal-title":"Infect Immun"},{"issue":"3","key":"371_CR298","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/S1074-7613(03)00057-8","volume":"18","author":"T Usui","year":"2003","unstructured":"Usui T, Nishikomori R, Kitani A, Strober W (2003) GATA-3 suppresses Th1 development by downregulation of Stat4 and not through effects on IL-12Rbeta2 chain or T-bet. Immunity 18(3):415\u2013428","journal-title":"Immunity"},{"issue":"2","key":"371_CR299","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/j.immuni.2013.05.018","volume":"39","author":"J van Loosdregt","year":"2013","unstructured":"van Loosdregt J, Fleskens V, Fu J, Brenkman AB, Bekker CP, Pals CE, Meerding J, Berkers CR, Barbi J, Grone A, Sijts AJ, Maurice MM, Kalkhoven E, Prakken BJ, Ovaa H, Pan F, Zaiss DM, Coffer PJ (2013) Stabilization of the transcription factor Foxp3 by the deubiquitinase USP7 increases Treg-cell-suppressive capacity. Immunity 39(2):259\u2013271. doi:10.1016\/j.immuni.2013.05.018","journal-title":"Immunity"},{"issue":"1","key":"371_CR300","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1084\/jem.20081438","volume":"206","author":"M Veldhoen","year":"2009","unstructured":"Veldhoen M, Hirota K, Christensen J, O\u2019Garra A, Stockinger B (2009) Natural agonists for aryl hydrocarbon receptor in culture medium are essential for optimal differentiation of Th17 T cells. J Exp Med 206(1):43\u201349. doi:10.1084\/jem.20081438","journal-title":"J Exp Med"},{"issue":"7191","key":"371_CR301","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1038\/nature06881","volume":"453","author":"M Veldhoen","year":"2008","unstructured":"Veldhoen M, Hirota K, Westendorf AM, Buer J, Dumoutier L, Renauld JC, Stockinger B (2008) The aryl hydrocarbon receptor links TH17-cell-mediated autoimmunity to environmental toxins. Nature 453(7191):106\u2013109. doi:10.1038\/nature06881","journal-title":"Nature"},{"issue":"12","key":"371_CR302","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1038\/ni.1659","volume":"9","author":"M Veldhoen Veldhoen","year":"2008","unstructured":"Veldhoen Veldhoen M, Uyttenhove C, van Snick J, Helmby H, Westendorf A, Buer J, Martin B, Wilhelm C, Stockinger B (2008) Transforming growth factor-beta \u2018reprograms\u2019 the differentiation of T helper 2 cells and promotes an interleukin 9-producing subset. Nat Immunol 9(12):1341\u20131346","journal-title":"Nat Immunol"},{"issue":"10","key":"371_CR303","doi-asserted-by":"crossref","first-page":"5632","DOI":"10.1128\/JVI.77.10.5632-5638.2003","volume":"77","author":"S Vigneau","year":"2003","unstructured":"Vigneau S, Rohrlich PS, Brahic M, Bureau JF (2003) Tmevpg1, a candidate gene for the control of Theiler\u2019s virus persistence, could be implicated in the regulation of gamma interferon. J Virol 77(10):5632\u20135638","journal-title":"J Virol"},{"issue":"5","key":"371_CR304","doi-asserted-by":"publisher","first-page":"1452","DOI":"10.1002\/art.30238","volume":"63","author":"J Vojinovic","year":"2011","unstructured":"Vojinovic J, Damjanov N, D\u2019Urzo C, Furlan A, Susic G, Pasic S, Iagaru N, Stefan M, Dinarello CA (2011) Safety and efficacy of an oral histone deacetylase inhibitor in systemic-onset juvenile idiopathic arthritis. Arthritis Rheum 63(5):1452\u20131458. doi:10.1002\/art.30238","journal-title":"Arthritis Rheum"},{"issue":"12","key":"371_CR305","doi-asserted-by":"crossref","first-page":"4793","DOI":"10.1073\/pnas.0900408106","volume":"106","author":"KS Voo","year":"2009","unstructured":"Voo KS, Wang YH, Santori FR, Boggiano C, Wang YH, Arima K, Bover L, Hanabuchi S, Khalili J, Marinova E, Zheng B, Littman DR, Liu YJ (2009) Identification of IL-17-producing FOXP3+\u00a0regulatory T cells in humans. Proc Natl Acad Sci USA 106(12):4793\u20134798","journal-title":"Proc Natl Acad Sci USA"},{"issue":"10","key":"371_CR306","doi-asserted-by":"publisher","first-page":"4908","DOI":"10.4049\/jimmunol.1300433","volume":"191","author":"A Wang","year":"2013","unstructured":"Wang A, Pan D, Lee YH, Martinez GJ, Feng XH, Dong C (2013) Cutting edge: Smad2 and Smad4 regulate TGF-beta-mediated Il9 gene expression via EZH2 displacement. J Immunol 191(10):4908\u20134912. doi:10.4049\/jimmunol.1300433","journal-title":"J Immunol"},{"issue":"7351","key":"371_CR307","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1038\/nature10006","volume":"474","author":"D Wang","year":"2011","unstructured":"Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, Glass CK, Rosenfeld MG, Fu XD (2011a) Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474(7351):390\u2013394. doi:10.1038\/nature10006","journal-title":"Nature"},{"issue":"4","key":"371_CR308","doi-asserted-by":"publisher","first-page":"171","DOI":"10.3233\/DMA-2011-0766","volume":"30","author":"G Wang","year":"2011","unstructured":"Wang G, Kwan BC, Lai FM, Chow KM, Li PK, Szeto CC (2011b) Elevated levels of miR-146a and miR-155 in kidney biopsy and urine from patients with IgA nephropathy. Dis Markers 30(4):171\u2013179. doi:10.3233\/DMA-2011-0766","journal-title":"Dis Markers"},{"issue":"6","key":"371_CR311","doi-asserted-by":"publisher","first-page":"871","DOI":"10.1016\/j.immuni.2011.09.021","volume":"35","author":"R Wang","year":"2011","unstructured":"Wang R, Dillon CP, Shi LZ, Milasta S, Carter R, Finkelstein D, McCormick LL, Fitzgerald P, Chi H, Munger J, Green DR (2011c) The transcription factor Myc controls metabolic reprogramming upon T lymphocyte activation. Immunity 35(6):871\u2013882. doi:10.1016\/j.immuni.2011.09.021","journal-title":"Immunity"},{"issue":"3","key":"371_CR312","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.immuni.2011.08.012","volume":"35","author":"Y Wang","year":"2011","unstructured":"Wang Y, Su MA, Wan YY (2011d) An essential role of the transcription factor GATA-3 for the function of regulatory T cells. Immunity 35(3):337\u2013348. doi:10.1016\/j.immuni.2011.08.012","journal-title":"Immunity"},{"issue":"1","key":"371_CR309","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1002\/eji.200636435","volume":"37","author":"J Wang","year":"2007","unstructured":"Wang J, Ioan-Facsinay A, van der Voort EI, Huizinga TW, Toes RE (2007) Transient expression of FOXP3 in human activated nonregulatory CD4+\u00a0T cells. Eur J Immunol 37(1):129\u2013138. doi:10.1002\/eji.200636435","journal-title":"Eur J Immunol"},{"issue":"12","key":"371_CR310","doi-asserted-by":"publisher","first-page":"969","DOI":"10.1038\/nrd3031","volume":"8","author":"L Wang","year":"2009","unstructured":"Wang L, de Zoeten EF, Greene MI, Hancock WW (2009a) Immunomodulatory effects of deacetylase inhibitors: therapeutic targeting of FOXP3\u00a0+\u00a0regulatory T cells. Nat Rev Drug Discov 8(12):969\u2013981. doi:10.1038\/nrd3031","journal-title":"Nat Rev Drug Discov"},{"issue":"5","key":"371_CR313","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1016\/j.cell.2009.06.049","volume":"138","author":"Z Wang","year":"2009","unstructured":"Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K (2009b) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138(5):1019\u20131031. doi:10.1016\/j.cell.2009.06.049","journal-title":"Cell"},{"key":"371_CR314","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1146\/annurev.immunol.25.022106.141557","volume":"25","author":"CT Weaver","year":"2007","unstructured":"Weaver CT, Hatton RD, Mangan PR, Harrington LE (2007) IL-17 family cytokines and the expanding diversity of effector T cell lineages. Annu Rev Immunol 25:821\u2013852. doi:10.1146\/annurev.immunol.25.022106.141557","journal-title":"Annu Rev Immunol"},{"issue":"1","key":"371_CR315","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.immuni.2008.12.009","volume":"30","author":"G Wei","year":"2009","unstructured":"Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, Schones DE, Peng W, Sun HW, Paul WE, O\u2019Shea JJ, Zhao K (2009) Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+\u00a0T cells. Immunity 30(1):155\u2013167","journal-title":"Immunity"},{"issue":"1","key":"371_CR316","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1111\/j.1600-065X.2011.01017.x","volume":"241","author":"HL Weiner","year":"2011","unstructured":"Weiner HL, da Cunha AP, Quintana F, Wu H (2011) Oral tolerance. Immunol Rev 241(1):241\u2013259. doi:10.1111\/j.1600-065X.2011.01017.x","journal-title":"Immunol Rev"},{"issue":"5740","key":"371_CR317","doi-asserted-by":"publisher","first-page":"1570","DOI":"10.1126\/science.1115901","volume":"309","author":"AT Willingham","year":"2005","unstructured":"Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309(5740):1570\u20131573. doi:10.1126\/science.1115901","journal-title":"Science"},{"issue":"2","key":"371_CR318","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nri2487","volume":"9","author":"CB Wilson","year":"2009","unstructured":"Wilson CB, Rowell E, Sekimata M (2009) Epigenetic control of T-helper-cell differentiation. Nat Rev Immunol 9(2):91\u2013105","journal-title":"Nat Rev Immunol"},{"issue":"12","key":"371_CR319","doi-asserted-by":"crossref","first-page":"7377","DOI":"10.4049\/jimmunol.173.12.7377","volume":"173","author":"BR Winders","year":"2004","unstructured":"Winders BR, Schwartz RH, Bruniquel D (2004) A distinct region of the murine IFN-gamma promoter is hypomethylated from early T cell development through mature naive and Th1 cell differentiation, but is hypermethylated in Th2 cells. J Immunol 173(12):7377\u20137384","journal-title":"J Immunol"},{"issue":"11","key":"371_CR320","doi-asserted-by":"publisher","first-page":"4503","DOI":"10.1172\/JCI57456","volume":"121","author":"EA Wohlfert","year":"2011","unstructured":"Wohlfert EA, Grainger JR, Bouladoux N, Konkel JE, Oldenhove G, Ribeiro CH, Hall JA, Yagi R, Naik S, Bhairavabhotla R, Paul WE, Bosselut R, Wei G, Zhao K, Oukka M, Zhu J, Belkaid Y (2011) GATA3 controls Foxp3(+) regulatory T cell fate during inflammation in mice. J Clin Investig 121(11):4503\u20134515. doi:10.1172\/JCI57456","journal-title":"J Clin Investig"},{"issue":"7446","key":"371_CR321","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/nature11984","volume":"496","author":"C Wu","year":"2013","unstructured":"Wu C, Yosef N, Thalhamer T, Zhu C, Xiao S, Kishi Y, Regev A, Kuchroo VK (2013) Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1. Nature 496(7446):513\u2013517. doi:10.1038\/nature11984","journal-title":"Nature"},{"issue":"3","key":"371_CR322","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/j.immuni.2010.09.001","volume":"33","author":"L Xu","year":"2010","unstructured":"Xu L, Kitani A, Stuelten C, McGrady G, Fuss I, Strober W (2010) Positive and negative transcriptional regulation of the Foxp3 gene is mediated by access and binding of the Smad3 protein to enhancer I. Immunity 33(3):313\u2013325. doi:10.1016\/j.immuni.2010.09.001","journal-title":"Immunity"},{"key":"371_CR323","doi-asserted-by":"publisher","unstructured":"Yadav M, Louvet C, Davini D, Gardner JM, Martinez-Llordella M, Bailey-Bucktrout S, Anthony BA, Sverdrup FM, Head R, Kuster DJ, Ruminski P, Weiss D, Von Schack D, Bluestone JA (2012) Neuropilin-1 distinguishes natural and inducible regulatory T cells among regulatory T cell subsets in vivo. J Exp Med 209 (10):1713\u20131722, S1711\u20131719. doi:10.1084\/jem.20120822","DOI":"10.1084\/jem.20120822"},{"issue":"7299","key":"371_CR324","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1038\/nature09229","volume":"465","author":"S Yamanaka","year":"2010","unstructured":"Yamanaka S, Blau HM (2010) Nuclear reprogramming to a pluripotent state by three approaches. Nature 465(7299):704\u2013712. doi:10.1038\/nature09229","journal-title":"Nature"},{"issue":"10","key":"371_CR325","doi-asserted-by":"publisher","first-page":"1577","DOI":"10.1007\/s00018-012-0966-9","volume":"69","author":"H Yamane","year":"2012","unstructured":"Yamane H, Paul WE (2012) Memory CD4\u00a0+\u00a0T cells: fate determination, positive feedback and plasticity. Cell Mol Life Sci 69(10):1577\u20131583. doi:10.1007\/s00018-012-0966-9","journal-title":"Cell Mol Life Sci"},{"issue":"9","key":"371_CR326","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1084\/jem.20112218","volume":"209","author":"L Yang","year":"2012","unstructured":"Yang L, Boldin MP, Yu Y, Liu CS, Ea CK, Ramakrishnan P, Taganov KD, Zhao JL, Baltimore D (2012) miR-146a controls the resolution of T cell responses in mice. J Exp Med 209(9):1655\u20131670. doi:10.1084\/jem.20112218","journal-title":"J Exp Med"},{"issue":"1","key":"371_CR327","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.immuni.2008.05.007","volume":"29","author":"XO Yang","year":"2008","unstructured":"Yang XO, Nurieva R, Martinez GJ, Kang HS, Chung Y, Pappu BP, Shah B, Chang SH, Schluns KS, Watowich SS, Feng XH, Jetten AM, Dong C (2008a) Molecular antagonism and plasticity of regulatory and inflammatory T cell programs. Immunity 29(1):44\u201356","journal-title":"Immunity"},{"issue":"1","key":"371_CR328","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/j.immuni.2007.11.016","volume":"28","author":"XO Yang","year":"2008","unstructured":"Yang XO, Pappu BP, Nurieva R, Akimzhanov A, Kang HS, Chung Y, Ma L, Shah B, Panopoulos AD, Schluns KS, Watowich SS, Tian Q, Jetten AM, Dong C (2008b) T helper 17 lineage differentiation is programmed by orphan nuclear receptors ROR alpha and ROR gamma. Immunity 28(1):29\u201339. doi:10.1016\/j.immuni.2007.11.016","journal-title":"Immunity"},{"issue":"3","key":"371_CR329","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1038\/ni.1995","volume":"12","author":"XP Yang","year":"2011","unstructured":"Yang XP, Ghoreschi K, Steward-Tharp SM, Rodriguez-Canales J, Zhu J, Grainger JR, Hirahara K, Sun HW, Wei L, Vahedi G, Kanno Y, O\u2019Shea JJ, Laurence A (2011) Opposing regulation of the locus encoding IL-17 through direct, reciprocal actions of STAT3 and STAT5. Nat Immunol 12(3):247\u2013254. doi:10.1038\/ni.1995","journal-title":"Nat Immunol"},{"issue":"7446","key":"371_CR330","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1038\/nature11981","volume":"496","author":"N Yosef","year":"2013","unstructured":"Yosef N, Shalek AK, Gaublomme JT, Jin H, Lee Y, Awasthi A, Wu C, Karwacz K, Xiao S, Jorgolli M, Gennert D, Satija R, Shakya A, Lu DY, Trombetta JJ, Pillai MR, Ratcliffe PJ, Coleman ML, Bix M, Tantin D, Park H, Kuchroo VK, Regev A (2013) Dynamic regulatory network controlling TH17 cell differentiation. Nature 496(7446):461\u2013468. doi:10.1038\/nature11981","journal-title":"Nature"},{"issue":"8","key":"371_CR331","doi-asserted-by":"crossref","first-page":"3603","DOI":"10.4049\/jimmunol.153.8.3603","volume":"153","author":"HA Young","year":"1994","unstructured":"Young HA, Ghosh P, Ye J, Lederer J, Lichtman A, Gerard JR, Penix L, Wilson CB, Melvin AJ, McGurn ME et al (1994) Differentiation of the T helper phenotypes by analysis of the methylation state of the IFN-gamma gene. J Immunol 153(8):3603\u20133610","journal-title":"J Immunol"},{"issue":"3","key":"371_CR332","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1016\/j.immuni.2009.07.002","volume":"31","author":"D Yu","year":"2009","unstructured":"Yu D, Rao S, Tsai LM, Lee SK, He Y, Sutcliffe EL, Srivastava M, Linterman M, Zheng L, Simpson N, Ellyard JI, Parish IA, Ma CS, Li QJ, Parish CR, Mackay CR, Vinuesa CG (2009) The transcriptional repressor Bcl-6 directs T follicular helper cell lineage commitment. Immunity 31(3):457\u2013468. doi:10.1016\/j.immuni.2009.07.002","journal-title":"Immunity"},{"issue":"34","key":"371_CR333","doi-asserted-by":"crossref","first-page":"21597","DOI":"10.1074\/jbc.272.34.21597","volume":"272","author":"DH Zhang","year":"1997","unstructured":"Zhang DH, Cohn L, Ray P, Bottomly K, Ray A (1997) Transcription factor GATA-3 is differentially expressed in murine Th1 and Th2 cells and controls Th2-specific expression of the interleukin-5 gene. J Biol Chem 272(34):21597\u201321603","journal-title":"J Biol Chem"},{"issue":"7282","key":"371_CR334","doi-asserted-by":"publisher","first-page":"808","DOI":"10.1038\/nature08750","volume":"463","author":"Y Zheng","year":"2010","unstructured":"Zheng Y, Josefowicz S, Chaudhry A, Peng XP, Forbush K, Rudensky AY (2010) Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate. Nature 463(7282):808\u2013812. doi:10.1038\/nature08750","journal-title":"Nature"},{"issue":"7130","key":"371_CR335","doi-asserted-by":"publisher","first-page":"936","DOI":"10.1038\/nature05563","volume":"445","author":"Y Zheng","year":"2007","unstructured":"Zheng Y, Josefowicz SZ, Kas A, Chu TT, Gavin MA, Rudensky AY (2007) Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells. Nature 445(7130):936\u2013940. doi:10.1038\/nature05563","journal-title":"Nature"},{"issue":"5","key":"371_CR336","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/ni1455","volume":"8","author":"Y Zheng","year":"2007","unstructured":"Zheng Y, Rudensky AY (2007) Foxp3 in control of the regulatory T cell lineage. Nat Immunol 8(5):457\u2013462","journal-title":"Nat Immunol"},{"issue":"5","key":"371_CR337","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.immuni.2009.05.001","volume":"30","author":"L Zhou","year":"2009","unstructured":"Zhou L, Chong MM, Littman DR (2009a) Plasticity of CD4\u00a0+\u00a0T cell lineage differentiation. Immunity 30(5):646\u2013655","journal-title":"Immunity"},{"issue":"9","key":"371_CR338","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1038\/ni1488","volume":"8","author":"L Zhou","year":"2007","unstructured":"Zhou L, Ivanov II, Spolski R, Min R, Shenderov K, Egawa T, Levy DE, Leonard WJ, Littman DR (2007) IL-6 programs T(H)-17 cell differentiation by promoting sequential engagement of the IL-21 and IL-23 pathways. Nat Immunol 8(9):967\u2013974","journal-title":"Nat Immunol"},{"issue":"7192","key":"371_CR339","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1038\/nature06878","volume":"453","author":"L Zhou","year":"2008","unstructured":"Zhou L, Lopes JE, Chong MM, Ivanov II, Min R, Victora GD, Shen Y, Du J, Rubtsov YP, Rudensky AY, Ziegler SF, Littman DR (2008) TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function. Nature 453(7192):236\u2013240","journal-title":"Nature"},{"issue":"9","key":"371_CR340","doi-asserted-by":"publisher","first-page":"1000","DOI":"10.1038\/ni.1774","volume":"10","author":"X Zhou","year":"2009","unstructured":"Zhou X, Bailey-Bucktrout SL, Jeker LT, Penaranda C, Martinez-Llordella M, Ashby M, Nakayama M, Rosenthal W, Bluestone JA (2009b) Instability of the transcription factor Foxp3 leads to the generation of pathogenic memory T cells in vivo. Nat Immunol 10(9):1000\u20131007. doi:10.1038\/ni.1774","journal-title":"Nat Immunol"},{"issue":"1","key":"371_CR341","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1111\/j.1600-065X.2010.00951.x","volume":"238","author":"J Zhu","year":"2010","unstructured":"Zhu J, Paul WE (2010) Peripheral CD4+\u00a0T-cell differentiation regulated by networks of cytokines and transcription factors. Immunol Rev 238(1):247\u2013262. doi:10.1111\/j.1600-065X.2010.00951.x","journal-title":"Immunol Rev"},{"key":"371_CR342","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1146\/annurev-immunol-030409-101212","volume":"28","author":"J Zhu","year":"2010","unstructured":"Zhu J, Yamane H, Paul WE (2010) Differentiation of effector CD4 T cell populations (*). Annu Rev Immunol 28:445\u2013489. doi:10.1146\/annurev-immunol-030409-101212","journal-title":"Annu Rev Immunol"},{"issue":"7395","key":"371_CR343","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1038\/nature10957","volume":"484","author":"CE Zielinski","year":"2012","unstructured":"Zielinski CE, Mele F, Aschenbrenner D, Jarrossay D, Ronchi F, Gattorno M, Monticelli S, Lanzavecchia A, Sallusto F (2012) Pathogen-induced human TH17 cells produce IFN-gamma or IL-10 and are regulated by IL-1beta. Nature 484(7395):514\u2013518. doi:10.1038\/nature10957","journal-title":"Nature"}],"container-title":["Current Topics in Microbiology and Immunology","Transcriptional Control of Lineage Differentiation in Immune Cells"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/82_2014_371","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,20]],"date-time":"2023-02-20T03:40:40Z","timestamp":1676864440000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/82_2014_371"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014]]},"ISBN":["9783319073941","9783319073958"],"references-count":342,"URL":"https:\/\/doi.org\/10.1007\/82_2014_371","relation":{},"ISSN":["0070-217X","2196-9965"],"issn-type":[{"value":"0070-217X","type":"print"},{"value":"2196-9965","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014]]},"assertion":[{"value":"16 May 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}