{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T07:05:29Z","timestamp":1792047929852,"version":"4.4.0"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2017,3,13]],"date-time":"2017-03-13T00:00:00Z","timestamp":1489363200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2017,3,13]],"date-time":"2017-03-13T00:00:00Z","timestamp":1489363200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Immunol"],"published-print":{"date-parts":[[2017,5]]},"DOI":"10.1038\/ni.3706","type":"journal-article","created":{"date-parts":[[2017,3,13]],"date-time":"2017-03-13T18:42:08Z","timestamp":1489430528000},"page":"573-582","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":247,"title":["Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation"],"prefix":"10.1038","volume":"18","author":[{"given":"Bingfei","family":"Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3454-7357","authenticated-orcid":false,"given":"Kai","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J Justin","family":"Milner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clara","family":"Toma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Runqiang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James P","family":"Scott-Browne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renata M","family":"Pereira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6484-6262","authenticated-orcid":false,"given":"Shane","family":"Crotty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John T","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew E","family":"Pipkin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ananda W","family":"Goldrath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,3,13]]},"reference":[{"key":"BFni3706_CR1","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1126\/science.272.5258.54","volume":"272","author":"R Ahmed","year":"1996","unstructured":"Ahmed, R. & Gray, D. Immunological memory and protective immunity: understanding their relation. Science 272, 54\u201360 (1996).","journal-title":"Science"},{"key":"BFni3706_CR2","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.immuni.2007.07.010","volume":"27","author":"NS Joshi","year":"2007","unstructured":"Joshi, N.S. et al. Inflammation directs memory precursor and short-lived effector CD8+ T cell fates via the graded expression of T-bet transcription factor. Immunity 27, 281\u2013295 (2007).","journal-title":"Immunity"},{"key":"BFni3706_CR3","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1038\/ni1009","volume":"4","author":"SM Kaech","year":"2003","unstructured":"Kaech, S.M. et al. Selective expression of the interleukin 7 receptor identifies effector CD8 T cells that give rise to long-lived memory cells. Nat. Immunol. 4, 1191\u20131198 (2003).","journal-title":"Nat. Immunol."},{"key":"BFni3706_CR4","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.immuni.2010.08.002","volume":"33","author":"X Zhou","year":"2010","unstructured":"Zhou, X. et al. Differentiation and persistence of memory CD8+ T cells depend on T cell factor 1. Immunity 33, 229\u2013240 (2010).","journal-title":"Immunity"},{"key":"BFni3706_CR5","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1038\/ni.3031","volume":"15","author":"JT Chang","year":"2014","unstructured":"Chang, J.T., Wherry, E.J. & Goldrath, A.W. Molecular regulation of effector and memory T cell differentiation. Nat. Rev. Immunol. 15, 1104\u20131115 (2014).","journal-title":"Nat. Rev. Immunol."},{"key":"BFni3706_CR6","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","volume":"10","author":"JD Buenrostro","year":"2013","unstructured":"Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y. & Greenleaf, W.J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213\u20131218 (2013).","journal-title":"Nat. Methods"},{"key":"BFni3706_CR7","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/nri3884","volume":"15","author":"D Winter","year":"2015","unstructured":"Winter, D. et al. Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape. Nat. Rev. Immunol. 15, 585\u2013594 (2015).","journal-title":"Nat. Rev. Immunol."},{"key":"BFni3706_CR8","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1016\/j.cell.2012.04.040","volume":"150","author":"S Neph","year":"2010","unstructured":"Neph, S. et al. Circuitry and dynamics of human transcription factor regulatory networks. Cell 150, 1274\u20131286 (2010).","journal-title":"Cell"},{"key":"BFni3706_CR9","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/nature11243","volume":"488","author":"Y Shen","year":"2012","unstructured":"Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116\u2013120 (2012).","journal-title":"Nature"},{"key":"BFni3706_CR10","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/nrg3207","volume":"13","author":"F Spitz","year":"2012","unstructured":"Spitz, F. & Furlong, E.E.M. Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet. 13, 613\u2013626 (2012).","journal-title":"Nat. Rev. Genet."},{"key":"BFni3706_CR11","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1016\/j.molcel.2013.01.038","volume":"49","author":"E Calo","year":"2013","unstructured":"Calo, E. & Wysocka, J. Modification of enhancer chromatin: what, how, and why? Mol. Cell 49, 825\u2013837 (2013).","journal-title":"Mol. Cell"},{"key":"BFni3706_CR12","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1126\/science.1256271","volume":"345","author":"D Lara-Astiaso","year":"2014","unstructured":"Lara-Astiaso, D. et al. Chromatin state dynamics during blood formation. Science 345, 943\u2013949 (2014).","journal-title":"Science"},{"key":"BFni3706_CR13","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1016\/j.cell.2014.11.018","volume":"159","author":"Y Lavin","year":"2014","unstructured":"Lavin, Y. et al. Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. Cell 159, 1312\u20131326 (2014).","journal-title":"Cell"},{"key":"BFni3706_CR14","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1016\/j.immuni.2009.05.006","volume":"30","author":"Y Araki","year":"2009","unstructured":"Araki, Y. et al. Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells. Immunity 30, 912\u2013925 (2009).","journal-title":"Immunity"},{"key":"BFni3706_CR15","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1016\/j.immuni.2014.11.001","volume":"41","author":"BE Russ","year":"2014","unstructured":"Russ, B.E. et al. Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8+ T cell differentiation. Immunity 41, 853\u2013865 (2014).","journal-title":"Immunity"},{"key":"BFni3706_CR16","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nature07829","volume":"459","author":"ND Heintzman","year":"2009","unstructured":"Heintzman, N.D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108\u2013112 (2009).","journal-title":"Nature"},{"key":"BFni3706_CR17","first-page":"997","volume":"29","author":"JA Best","year":"2013","unstructured":"Best, J.A. et al. Transcriptional insights into the CD8+ T cell response to infection and memory T cell formation. Nat. Immunol. 29, 997\u20131003 (2013).","journal-title":"Nat. Immunol."},{"key":"BFni3706_CR18","doi-asserted-by":"crossref","first-page":"3704","DOI":"10.1182\/blood-2008-06-160945","volume":"112","author":"M Rubinstein","year":"2008","unstructured":"Rubinstein, M. et al. IL-7 and IL-15 differentially regulate CD8+ T-cell subsets during contraction of the immune response. Blood 112, 3704\u20133712 (2008).","journal-title":"Blood"},{"key":"BFni3706_CR19","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1038\/ni.2158","volume":"12","author":"CY Yang","year":"2011","unstructured":"Yang, C.Y. et al. The transcriptional regulators Id2 and Id3 control the formation of distinct memory CD8+ T cell subsets. Nat. Immunol. 12, 1221\u20131229 (2011).","journal-title":"Nat. Immunol."},{"key":"BFni3706_CR20","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1038\/ni.2086","volume":"12","author":"M Miyazaki","year":"2012","unstructured":"Miyazaki, M. et al. The opposing roles of E2A and Id3 that orchestrate and enforce the na\u00efve T cell fate. Nat. Immunol. 12, 992\u20131001 (2012).","journal-title":"Nat. Immunol."},{"key":"BFni3706_CR21","doi-asserted-by":"crossref","first-page":"e1002968","DOI":"10.1371\/journal.pcbi.1002968","volume":"9","author":"N Rajagopal","year":"2013","unstructured":"Rajagopal, N. et al. RFECS: A random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput. Biol. 9, e1002968 (2013).","journal-title":"PLoS Comput. Biol."},{"key":"BFni3706_CR22","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.4049\/jimmunol.1400488","volume":"193","author":"J Chaix","year":"2014","unstructured":"Chaix, J. et al. Cutting edge: CXCR4 is critical for CD8+ memory T cell homeostatic self-renewal but not rechallenge self-renewal. J. Immunol. 193, 1013\u20131016 (2014).","journal-title":"J. Immunol."},{"key":"BFni3706_CR23","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.1630","volume":"28","author":"CY McLean","year":"2010","unstructured":"McLean, C.Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495\u2013501 (2010).","journal-title":"Nat. Biotechnol."},{"key":"BFni3706_CR24","doi-asserted-by":"crossref","first-page":"11013","DOI":"10.1073\/pnas.1510119112","volume":"112","author":"C Ma","year":"2015","unstructured":"Ma, C. & Zhang, N. Transforming growth factor-\u03b2 signaling is constantly shaping memory T-cell population. Proc. Natl. Acad. Sci. USA 112, 11013\u201311017 (2015).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFni3706_CR25","doi-asserted-by":"crossref","first-page":"2027","DOI":"10.1084\/jem.20150194","volume":"212","author":"KD Omilusik","year":"2015","unstructured":"Omilusik, K.D. et al. Transcriptional repressor ZEB2 promotes terminal differentiation of CD8+ effector and memory T cell populations during infection. J. Exp. Med. 212, 2027\u20132039 (2015).","journal-title":"J. Exp. Med."},{"key":"BFni3706_CR26","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1084\/jem.20150186","volume":"212","author":"CX Dominguez","year":"2015","unstructured":"Dominguez, C.X. et al. The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation in response to LCMV viral infection. J. Exp. Med. 212, 2041\u20132056 (2015).","journal-title":"J. Exp. Med."},{"key":"BFni3706_CR27","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1038\/ni1268","volume":"6","author":"AM Intlekofer","year":"2005","unstructured":"Intlekofer, A.M. et al. Effector and memory CD8+ T cell fate coupled by T-bet and eomesodermin. Nat. Immunol. 6, 1236\u20131244 (2005).","journal-title":"Nat. Immunol."},{"key":"BFni3706_CR28","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/ni.2570","volume":"14","author":"Y Kidani","year":"2013","unstructured":"Kidani, Y. et al. Sterol regulatory element-binding proteins are essential for the metabolic programming of effector T cells and adaptive immunity. Nat. Immunol. 14, 489\u2013499 (2013).","journal-title":"Nat. Immunol."},{"key":"BFni3706_CR29","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1038\/ni.2834","volume":"15","author":"M Kurachi","year":"2014","unstructured":"Kurachi, M. et al. The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells. Nat. Immunol. 15, 373\u2013383 (2014).","journal-title":"Nat. Immunol."},{"key":"BFni3706_CR30","doi-asserted-by":"crossref","first-page":"2722","DOI":"10.4049\/jimmunol.1201150","volume":"189","author":"X Zhou","year":"2012","unstructured":"Zhou, X. & Xue, H. Generation of memory precursors and functional memory CD8+ T cells depends on TCF-1 and LEF-1. J. Immunol. 189, 2722\u20132726 (2012).","journal-title":"J. Immunol."},{"key":"BFni3706_CR31","doi-asserted-by":"crossref","first-page":"2031","DOI":"10.1002\/eji.201242497","volume":"42","author":"LM D'Cruz","year":"2012","unstructured":"D'Cruz, L.M., Lind, K.C., Wu, B.B., Fujimoto, J.K. & Goldrath, A.W. Loss of E protein transcription factors E2A and HEB delays memory-precursor formation during the CD8+ T-cell immune response. Eur. J. Immunol. 42, 2031\u20132041 (2012).","journal-title":"Eur. J. Immunol."},{"key":"BFni3706_CR32","doi-asserted-by":"crossref","first-page":"4370","DOI":"10.1002\/j.1460-2075.1994.tb06757.x","volume":"13","author":"M Rinc\u00f3n","year":"1994","unstructured":"Rinc\u00f3n, M. & Flavell, R.a. AP-1 transcriptional activity requires both T-cell receptor-mediated and co-stimulatory signals in primary T lymphocytes. EMBO J. 13, 4370\u20134381 (1994).","journal-title":"EMBO J."},{"key":"BFni3706_CR33","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1016\/j.immuni.2012.08.021","volume":"37","author":"T Doering","year":"2012","unstructured":"Doering, T. et al. Network analysis reveals centrally connected genes and pathways involved in CD8+ T Cell exhaustion versus memory. Immunity 37, 1130\u20131144 (2012).","journal-title":"Immunity"},{"key":"BFni3706_CR34","doi-asserted-by":"crossref","first-page":"2830","DOI":"10.1038\/ncomms3830","volume":"4","author":"G Hu","year":"2013","unstructured":"Hu, G. & Chen, J. A genome-wide regulatory network identifies key transcription factors for memory CD8+ T-cell development. Nat. Commun. 4, 2830 (2013).","journal-title":"Nat. Commun."},{"key":"BFni3706_CR35","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1126\/science.1065543","volume":"295","author":"SJ Szabo","year":"2002","unstructured":"Szabo, S.J. et al. Distinct effects of T-bet in TH1 lineage commitment and IFN-\u03b3 production in CD4 and CD8 T cells. Science 295, 338\u2013342 (2002).","journal-title":"Science"},{"key":"BFni3706_CR36","doi-asserted-by":"crossref","first-page":"3432","DOI":"10.1182\/blood-2005-04-1393","volume":"106","author":"GM Lord","year":"2005","unstructured":"Lord, G.M. et al. T-bet is required for optimal proinflammatory CD4+ T-cell trafficking. Blood 106, 3432\u20133439 (2005).","journal-title":"Blood"},{"key":"BFni3706_CR37","first-page":"1","volume":"54","author":"L Page","year":"1998","unstructured":"Page, L., Brin, S., Motwani, R. & Winograd, T. The PageRank citation ranking: bringing order to the web. World Wide Web (Bussum) 54, 1\u201317 (1998).","journal-title":"World Wide Web (Bussum)"},{"key":"BFni3706_CR38","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1016\/j.immuni.2011.09.017","volume":"35","author":"W Cui","year":"2011","unstructured":"Cui, W., Liu, Y., Weinstein, J.S., Craft, J. & Kaech, S.M. An interleukin-21- interleukin-10-STAT3 pathway is critical for functional maturation of memory CD8+ T cells. Immunity 35, 792\u2013805 (2011).","journal-title":"Immunity"},{"key":"BFni3706_CR39","doi-asserted-by":"crossref","first-page":"839","DOI":"10.15252\/msb.20156236","volume":"11","author":"ML Arrieta-Ortiz","year":"2015","unstructured":"Arrieta-Ortiz, M.L. et al. An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network. Mol. Syst. Biol. 11, 839 (2015).","journal-title":"Mol. Syst. Biol."},{"key":"BFni3706_CR40","doi-asserted-by":"crossref","first-page":"10789","DOI":"10.1038\/ncomms10789","volume":"7","author":"SS Hwang","year":"2016","unstructured":"Hwang, S.S. et al. YY1 inhibits differentiation and function of regulatory T cells by blocking Foxp3 expression and activity. Nat. Commun. 7, 10789 (2016).","journal-title":"Nat. Commun."},{"key":"BFni3706_CR41","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1073\/pnas.1214682110","volume":"110","author":"SS Hwang","year":"2013","unstructured":"Hwang, S.S. et al. Transcription factor YY1 is essential for regulation of the Th2 cytokine locus and for Th2 cell differentiation. Proc. Natl. Acad. Sci. USA 110, 276\u2013281 (2013).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFni3706_CR42","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1101\/gad.1529307","volume":"21","author":"H Liu","year":"2007","unstructured":"Liu, H. et al. Yin Yang 1 is a critical regulator of B-cell development. Genes Dev. 21, 1179\u20131189 (2007).","journal-title":"Genes Dev."},{"key":"BFni3706_CR43","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1007\/s00018-005-5390-y","volume":"63","author":"MJ Herold","year":"2006","unstructured":"Herold, M.J., McPherson, K.G. & Reichardt, H.M. Glucocorticoids in T cell apoptosis and function. Cell. Mol. Life Sci. 63, 60\u201372 (2006).","journal-title":"Cell. Mol. Life Sci."},{"key":"BFni3706_CR44","doi-asserted-by":"crossref","first-page":"2212","DOI":"10.4049\/jimmunol.168.5.2212","volume":"168","author":"D Franchimont","year":"2002","unstructured":"Franchimont, D. et al. Positive effects of glucocorticoids on T cell function by up-regulation of IL-7 receptor alpha. J. Immunol. 168, 2212\u20132218 (2002).","journal-title":"J. Immunol."},{"key":"BFni3706_CR45","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1016\/j.mad.2004.06.010","volume":"125","author":"KA Smoak","year":"2004","unstructured":"Smoak, K.A. & Cidlowski, J.A. Mechanisms of glucocorticoid receptor signaling during inflammation. Mech. Ageing Dev. 125, 697\u2013706 (2004).","journal-title":"Mech. Ageing Dev."},{"key":"BFni3706_CR46","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1210\/me.2003-0421","volume":"18","author":"Q Wang","year":"2004","unstructured":"Wang, Q. et al. Equilibrium interactions of corepressors and coactivators with agonist and antagonist complexes of glucocorticoid receptors. Mol. Endocrinol. 18, 1376\u20131395 (2004).","journal-title":"Mol. Endocrinol."},{"key":"BFni3706_CR47","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1038\/nature14233","volume":"518","author":"AM Tsankov","year":"2015","unstructured":"Tsankov, A.M. et al. Transcription factor binding dynamics during human ES cell differentiation. Nature 518, 344\u2013349 (2015).","journal-title":"Nature"},{"key":"BFni3706_CR48","first-page":"1","volume":"7","author":"K Zhang","year":"2016","unstructured":"Zhang, K., Li, N., Ainsworth, R. & Wang, W. Systematic identification of protein combinations mediating chromatin looping. Nat. Commun. 7, 1\u201311 (2016).","journal-title":"Nat. Commun."},{"key":"BFni3706_CR49","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/nature14222","volume":"518","author":"JR Dixon","year":"2015","unstructured":"Dixon, J.R. et al. Chromatin architecture reorganization during stem cell differentiation. Nature 518, 331\u2013336 (2015).","journal-title":"Nature"},{"key":"BFni3706_CR50","doi-asserted-by":"crossref","first-page":"10812","DOI":"10.1038\/ncomms10812","volume":"7","author":"Y Zhu","year":"2016","unstructured":"Zhu, Y. et al. Constructing 3D interaction maps from 1D epigenomes. Nat. Commun. 7, 10812 (2016).","journal-title":"Nat. Commun."},{"key":"BFni3706_CR51","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.immuni.2014.08.002","volume":"41","author":"R Chen","year":"2014","unstructured":"Chen, R. et al. In vivo RNA interference screens identify regulators of antiviral CD4+ and CD8+ T cell differentiation. Immunity 41, 325\u2013338 (2014).","journal-title":"Immunity"},{"key":"BFni3706_CR52","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"BFni3706_CR53","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"BFni3706_CR54","doi-asserted-by":"crossref","first-page":"D110","DOI":"10.1093\/nar\/gkv1176","volume":"44","author":"A Mathelier","year":"2016","unstructured":"Mathelier, A. et al. JASPAR 2016: A major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 44, D110\u2013D115 (2016).","journal-title":"Nucleic Acids Res."},{"key":"BFni3706_CR55","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1093\/nar\/gkn660","volume":"37","author":"DE Newburger","year":"2009","unstructured":"Newburger, D.E. & Bulyk, M.L. UniPROBE: An online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res. 37, 77\u201382 (2009).","journal-title":"Nucleic Acids Res."},{"key":"BFni3706_CR56","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/j.cell.2012.12.009","volume":"152","author":"A Jolma","year":"2013","unstructured":"Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327\u2013339 (2013).","journal-title":"Cell"},{"key":"BFni3706_CR57","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","volume":"27","author":"CE Grant","year":"2011","unstructured":"Grant, C.E., Bailey, T.L. & Noble, W.S. FIMO: Scanning for occurrences of a given motif. Bioinformatics 27, 1017\u20131018 (2011).","journal-title":"Bioinformatics"},{"key":"BFni3706_CR58","first-page":"271","volume":"12","author":"G Jeh","year":"2003","unstructured":"Jeh, G. & Widom, J. Scaling personalized web search. Proc. 2003 Int. World Wide Web Conf. (WWW'03) 12, 271\u2013279 (2003).","journal-title":"Proc. 2003 Int. World Wide Web Conf. (WWW'03)"}],"updated-by":[{"DOI":"10.1038\/ni0617-705b","type":"erratum","label":"Erratum","source":"publisher","updated":{"date-parts":[[2017,6,1]],"date-time":"2017-06-01T00:00:00Z","timestamp":1496275200000}}],"container-title":["Nature Immunology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/ni.3706.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/ni.3706","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/ni.3706.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T22:13:41Z","timestamp":1684448021000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/ni.3706"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3,13]]},"references-count":58,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2017,5]]}},"alternative-id":["BFni3706"],"URL":"https:\/\/doi.org\/10.1038\/ni.3706","relation":{"erratum":[{"id-type":"doi","id":"10.1038\/ni0617-705b","asserted-by":"object"}]},"ISSN":["1529-2908","1529-2916"],"issn-type":[{"value":"1529-2908","type":"print"},{"value":"1529-2916","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3,13]]},"assertion":[{"value":"10 October 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 February 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 March 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 March 2017","order":4,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Erratum","order":5,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"In the version of this article initially published online, some labels in Figure 2 were illegible or incorrect. Those should read \"Enhancers (\u00d7 103)\" along the top and \"TE, MP and M\" (top to bottom) along the left margin of Figure 2a; \"N, TE, MP and M\" (left to right) above the plot in Figure 2b; and \"GO\" below the plot in Figure 2c. Also, in the third sentence of the final paragraph of the final subsection of Results (Validation of PageRank-predicted TFs), the description of the control cells (\"shCon-transfected\") was incorrect. The correct text is \"...lower among shNr3c1-transduced cells than among shCon-transduced cells...\". The errors have been corrected in the print, PDF and HTML versions of this article.","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}