{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T07:08:05Z","timestamp":1791616085619,"version":"4.3.4"},"reference-count":67,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2017,2,27]],"date-time":"2017-02-27T00:00:00Z","timestamp":1488153600000},"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":["Nat Immunol"],"published-print":{"date-parts":[[2017,4]]},"DOI":"10.1038\/ni.3694","type":"journal-article","created":{"date-parts":[[2017,3,2]],"date-time":"2017-03-02T04:31:13Z","timestamp":1488429073000},"page":"442-455","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":126,"title":["Essential role for the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells"],"prefix":"10.1038","volume":"18","author":[{"given":"Taras","family":"Kreslavsky","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bojan","family":"Vilagos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiromi","family":"Tagoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela Kostanova","family":"Poliakova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanja A","family":"Schwickert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam","family":"W\u00f6hner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Jaritz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siegfried","family":"Weiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reshma","family":"Taneja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moritz J","family":"Rossner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meinrad","family":"Busslinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,2,27]]},"reference":[{"key":"BFni3694_CR1","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1084\/jem.157.1.202","volume":"157","author":"K Hayakawa","year":"1983","unstructured":"Hayakawa, K., Hardy, R.R., Parks, D.R. & Herzenberg, L.A. The \u201cLy-1 B\u201d cell subpopulation in normal immunodefective, and autoimmune mice. J. Exp. Med. 157, 202\u2013218 (1983).","journal-title":"J. Exp. Med."},{"key":"BFni3694_CR2","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1038\/nri2901","volume":"11","author":"N Baumgarth","year":"2011","unstructured":"Baumgarth, N. The double life of a B-1 cell: self-reactivity selects for protective effector functions. Nat. Rev. Immunol. 11, 34\u201346 (2011).","journal-title":"Nat. Rev. Immunol."},{"key":"BFni3694_CR3","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/j.immuni.2011.11.017","volume":"36","author":"E Montecino-Rodriguez","year":"2012","unstructured":"Montecino-Rodriguez, E. & Dorshkind, K. B-1 B cell development in the fetus and adult. Immunity 36, 13\u201321 (2012).","journal-title":"Immunity"},{"key":"BFni3694_CR4","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/ni1036","volume":"5","author":"S Casola","year":"2004","unstructured":"Casola, S. et al. B cell receptor signal strength determines B cell fate. Nat. Immunol. 5, 317\u2013327 (2004).","journal-title":"Nat. Immunol."},{"key":"BFni3694_CR5","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1146\/annurev.immunol.19.1.595","volume":"19","author":"RR Hardy","year":"2001","unstructured":"Hardy, R.R. & Hayakawa, K. B cell development pathways. Annu. Rev. Immunol. 19, 595\u2013621 (2001).","journal-title":"Annu. Rev. Immunol."},{"key":"BFni3694_CR6","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1038\/ni1480","volume":"8","author":"A Hoffmann","year":"2007","unstructured":"Hoffmann, A. et al. Siglec-G is a B1 cell-inhibitory receptor that controls expansion and calcium signaling of the B1 cell population. Nat. Immunol. 8, 695\u2013704 (2007).","journal-title":"Nat. Immunol."},{"key":"BFni3694_CR7","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1016\/S1074-7613(00)80124-7","volume":"11","author":"C Pan","year":"1999","unstructured":"Pan, C., Baumgarth, N. & Parnes, J.R. CD72-deficient mice reveal nonredundant roles of CD72 in B cell development and activation. Immunity 11, 495\u2013506 (1999).","journal-title":"Immunity"},{"key":"BFni3694_CR8","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1007\/s10875-010-9396-3","volume":"30","author":"CJ Binder","year":"2010","unstructured":"Binder, C.J. Natural IgM antibodies against oxidation-specific epitopes. J. Clin. Immunol. 30, 56\u201360 (2010).","journal-title":"J. Clin. Immunol."},{"key":"BFni3694_CR9","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1111\/j.0105-2896.2004.0098.x","volume":"197","author":"H Wang","year":"2004","unstructured":"Wang, H. & Clarke, S.H. Positive selection focuses the VH12 B-cell repertoire towards a single B1 specificity with survival function. Immunol. Rev. 197, 51\u201359 (2004).","journal-title":"Immunol. Rev."},{"key":"BFni3694_CR10","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/S0163-7827(02)00050-4","volume":"42","author":"C Sohlenkamp","year":"2003","unstructured":"Sohlenkamp, C., L\u00f3pez-Lara, I.M. & Geiger, O. Biosynthesis of phosphatidylcholine in bacteria. Prog. Lipid Res. 42, 115\u2013162 (2003).","journal-title":"Prog. Lipid Res."},{"key":"BFni3694_CR11","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1002\/eji.1830190315","volume":"19","author":"PA Lalor","year":"1989","unstructured":"Lalor, P.A., Herzenberg, L.A., Adams, S. & Stall, A.M. Feedback regulation of murine Ly-1 B cell development. Eur. J. Immunol. 19, 507\u2013513 (1989).","journal-title":"Eur. J. Immunol."},{"key":"BFni3694_CR12","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1016\/j.immuni.2016.07.014","volume":"45","author":"TA Kristiansen","year":"2016","unstructured":"Kristiansen, T.A. et al. Cellular barcoding links B-1a B cell potential to a fetal hematopoietic stem cell state at the single-cell level. Immunity 45, 346\u2013357 (2016).","journal-title":"Immunity"},{"key":"BFni3694_CR13","doi-asserted-by":"publisher","first-page":"e09083","DOI":"10.7554\/eLife.09083","volume":"4","author":"Y Yang","year":"2015","unstructured":"Yang, Y. et al. Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires. eLife 4, e09083 (2015).","journal-title":"eLife"},{"key":"BFni3694_CR14","doi-asserted-by":"publisher","first-page":"2133","DOI":"10.1002\/j.1460-2075.1990.tb07382.x","volume":"9","author":"H Gu","year":"1990","unstructured":"Gu, H., F\u00f6rster, I. & Rajewsky, K. Sequence homologies, N sequence insertion and JH gene utilization in VHDJH joining: implications for the joining mechanism and the ontogenetic timing of Ly1 B cell and B-CLL progenitor generation. EMBO J. 9, 2133\u20132140 (1990).","journal-title":"EMBO J."},{"key":"BFni3694_CR15","doi-asserted-by":"publisher","first-page":"4960","DOI":"10.1182\/blood-2009-04-218156","volume":"114","author":"S D\u00fcber","year":"2009","unstructured":"D\u00fcber, S. et al. Induction of B-cell development in adult mice reveals the ability of bone marrow to produce B-1a cells. Blood 114, 4960\u20134967 (2009).","journal-title":"Blood"},{"key":"BFni3694_CR16","doi-asserted-by":"publisher","first-page":"953","DOI":"10.1016\/0092-8674(89)90748-4","volume":"59","author":"LA Herzenberg","year":"1989","unstructured":"Herzenberg, L.A. & Herzenberg, L.A. Toward a layered immune system. Cell 59, 953\u2013954 (1989).","journal-title":"Cell"},{"key":"BFni3694_CR17","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/ni1301","volume":"7","author":"E Montecino-Rodriguez","year":"2006","unstructured":"Montecino-Rodriguez, E., Leathers, H. & Dorshkind, K. Identification of a B-1 B cell-specified progenitor. Nat. Immunol. 7, 293\u2013301 (2006).","journal-title":"Nat. Immunol."},{"key":"BFni3694_CR18","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1016\/j.immuni.2016.07.012","volume":"45","author":"E Montecino-Rodriguez","year":"2016","unstructured":"Montecino-Rodriguez, E. et al. Distinct genetic networks orchestrate the emergence of specific waves of fetal and adult B-1 and B-2 development. Immunity 45, 527\u2013539 (2016).","journal-title":"Immunity"},{"key":"BFni3694_CR19","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/0167-5699(93)90064-R","volume":"14","author":"G Haughton","year":"1993","unstructured":"Haughton, G., Arnold, L.W., Whitmore, A.C. & Clarke, S.H. B-1 cells are made, not born. Immunol. Today 14, 84\u201387 (1993).","journal-title":"Immunol. Today"},{"key":"BFni3694_CR20","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1126\/science.285.5424.113","volume":"285","author":"K Hayakawa","year":"1999","unstructured":"Hayakawa, K. et al. Positive selection of natural autoreactive B cells. Science 285, 113\u2013116 (1999).","journal-title":"Science"},{"key":"BFni3694_CR21","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1146\/annurev.immunol.20.100301.064833","volume":"20","author":"R Berland","year":"2002","unstructured":"Berland, R. & Wortis, H.H. Origins and functions of B-1 cells with notes on the role of CD5. Annu. Rev. Immunol. 20, 253\u2013300 (2002).","journal-title":"Annu. Rev. Immunol."},{"key":"BFni3694_CR22","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1084\/jem.20141510","volume":"212","author":"Y Zhou","year":"2015","unstructured":"Zhou, Y. et al. Lin28b promotes fetal B lymphopoiesis through the transcription factor Arid3a. J. Exp. Med. 212, 569\u2013580 (2015).","journal-title":"J. Exp. Med."},{"key":"BFni3694_CR23","doi-asserted-by":"publisher","first-page":"1195","DOI":"10.1126\/science.1216557","volume":"335","author":"J Yuan","year":"2012","unstructured":"Yuan, J., Nguyen, C.K., Liu, X., Kanellopoulou, C. & Muljo, S.A. Lin28b reprograms adult bone marrow hematopoietic progenitors to mediate fetal-like lymphopoiesis. Science 335, 1195\u20131200 (2012).","journal-title":"Science"},{"key":"BFni3694_CR24","doi-asserted-by":"crossref","first-page":"5273","DOI":"10.4049\/jimmunol.159.11.5273","volume":"159","author":"PO Humbert","year":"1997","unstructured":"Humbert, P.O. & Corcoran, L.M. oct-2 gene disruption eliminates the peritoneal B-1 lymphocyte lineage and attenuates B-2 cell maturation and function. J. Immunol. 159, 5273\u20135284 (1997).","journal-title":"J. Immunol."},{"key":"BFni3694_CR25","doi-asserted-by":"publisher","first-page":"E4119","DOI":"10.1073\/pnas.1415866111","volume":"111","author":"GK Pedersen","year":"2014","unstructured":"Pedersen, G.K. et al. B-1a transitional cells are phenotypically distinct and are lacking in mice deficient in I\u03baBNS. Proc. Natl. Acad. Sci. USA 111, E4119\u2013E4126 (2014).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFni3694_CR26","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1016\/B978-0-12-405943-6.00010-5","volume":"110","author":"Y Kato","year":"2014","unstructured":"Kato, Y., Kawamoto, T., Fujimoto, K. & Noshiro, M. DEC1\/STRA13\/SHARP2 and DEC2\/SHARP1 coordinate physiological processes, including circadian rhythms in response to environmental stimuli. Curr. Top. Dev. Biol. 110, 339\u2013372 (2014).","journal-title":"Curr. Top. Dev. Biol."},{"key":"BFni3694_CR27","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1016\/B978-0-12-405943-6.00009-9","volume":"110","author":"JR Ow","year":"2014","unstructured":"Ow, J.R., Tan, Y.H., Jin, Y., Bahirvani, A.G. & Taneja, R. Stra13 and Sharp-1, the non-grouchy regulators of development and disease. Curr. Top. Dev. Biol. 110, 317\u2013338 (2014).","journal-title":"Curr. Top. Dev. Biol."},{"key":"BFni3694_CR28","doi-asserted-by":"publisher","first-page":"1040","DOI":"10.1038\/ni721","volume":"2","author":"H Sun","year":"2001","unstructured":"Sun, H., Lu, B., Li, R.Q., Flavell, R.A. & Taneja, R. Defective T cell activation and autoimmune disorder in Stra13-deficient mice. Nat. Immunol. 2, 1040\u20131047 (2001).","journal-title":"Nat. Immunol."},{"key":"BFni3694_CR29","doi-asserted-by":"publisher","first-page":"1260","DOI":"10.1038\/ni.1821","volume":"10","author":"XO Yang","year":"2009","unstructured":"Yang, X.O. et al. Requirement for the basic helix-loop-helix transcription factor Dec2 in initial TH2 lineage commitment. Nat. Immunol. 10, 1260\u20131266 (2009).","journal-title":"Nat. Immunol."},{"key":"BFni3694_CR30","doi-asserted-by":"publisher","first-page":"3551","DOI":"10.1038\/ncomms4551","volume":"5","author":"C-C Lin","year":"2014","unstructured":"Lin, C.-C. et al. Bhlhe40 controls cytokine production by T cells and is essential for pathogenicity in autoimmune neuroinflammation. Nat. Commun. 5, 3551 (2014).","journal-title":"Nat. Commun."},{"key":"BFni3694_CR31","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1084\/jem.20112422","volume":"209","author":"B Vilagos","year":"2012","unstructured":"Vilagos, B. et al. Essential role of EBF1 in the generation and function of distinct mature B cell types. J. Exp. Med. 209, 775\u2013792 (2012).","journal-title":"J. Exp. Med."},{"key":"BFni3694_CR32","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1038\/ni1008-1091","volume":"9","author":"TS Heng","year":"2008","unstructured":"Heng, T.S. & Painter, M.W. The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091\u20131094 (2008).","journal-title":"Nat. Immunol."},{"key":"BFni3694_CR33","doi-asserted-by":"publisher","first-page":"e110310","DOI":"10.1371\/journal.pone.0110310","volume":"9","author":"PC Baier","year":"2014","unstructured":"Baier, P.C. et al. Mice lacking the circadian modulators SHARP1 and SHARP2 display altered sleep and mixed state endophenotypes of psychiatric disorders. PLoS One 9, e110310 (2014).","journal-title":"PLoS One"},{"key":"BFni3694_CR34","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1038\/nature01123","volume":"419","author":"S Honma","year":"2002","unstructured":"Honma, S. et al. Dec1 and Dec2 are regulators of the mammalian molecular clock. Nature 419, 841\u2013844 (2002).","journal-title":"Nature"},{"key":"BFni3694_CR35","doi-asserted-by":"publisher","first-page":"1201","DOI":"10.1084\/jem.20152002","volume":"213","author":"M W\u00f6hner","year":"2016","unstructured":"W\u00f6hner, M. et al. Molecular functions of the transcription factors E2A and E2\u20132 in controlling germinal center B cell and plasma cell development. J. Exp. Med. 213, 1201\u20131221 (2016).","journal-title":"J. Exp. Med."},{"key":"BFni3694_CR36","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1006\/bbrc.2002.6605","volume":"292","author":"M Seimiya","year":"2002","unstructured":"Seimiya, M. et al. Clast5\/Stra13 is a negative regulator of B lymphocyte activation. Biochem. Biophys. Res. Commun. 292, 121\u2013127 (2002).","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"BFni3694_CR37","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.1084\/jem.179.5.1585","volume":"179","author":"LW Arnold","year":"1994","unstructured":"Arnold, L.W., Pennell, C.A., McCray, S.K. & Clarke, S.H. Development of B-1 cells: segregation of phosphatidylcholine-specific B cells to the B-1 population occurs after immunoglobulin gene expression. J. Exp. Med. 179, 1585\u20131595 (1994).","journal-title":"J. Exp. Med."},{"key":"BFni3694_CR38","doi-asserted-by":"publisher","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":"BFni3694_CR39","doi-asserted-by":"publisher","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":"BFni3694_CR40","doi-asserted-by":"publisher","first-page":"3029","DOI":"10.1016\/j.molimm.2009.06.011","volume":"46","author":"NE Holodick","year":"2009","unstructured":"Holodick, N.E., Tumang, J.R. & Rothstein, T.L. Continual signaling is responsible for constitutive ERK phosphorylation in B-1a cells. Mol. Immunol. 46, 3029\u20133036 (2009).","journal-title":"Mol. Immunol."},{"key":"BFni3694_CR41","doi-asserted-by":"publisher","first-page":"30707","DOI":"10.1074\/jbc.M202460200","volume":"277","author":"S-C Wong","year":"2002","unstructured":"Wong, S.-C. et al. Peritoneal CD5+ B-1 cells have signaling properties similar to tolerant B cells. J. Biol. Chem. 277, 30707\u201330715 (2002).","journal-title":"J. Biol. Chem."},{"key":"BFni3694_CR42","doi-asserted-by":"publisher","first-page":"27181","DOI":"10.1074\/jbc.M704625200","volume":"282","author":"V Chew","year":"2007","unstructured":"Chew, V. & Lam, K.-P. Leupaxin negatively regulates B cell receptor signaling. J. Biol. Chem. 282, 27181\u201327191 (2007).","journal-title":"J. Biol. Chem."},{"key":"BFni3694_CR43","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1038\/376352a0","volume":"376","author":"RC Rickert","year":"1995","unstructured":"Rickert, R.C., Rajewsky, K. & Roes, J. Impairment of T-cell-dependent B-cell responses and B-1 cell development in CD19-deficient mice. Nature 376, 352\u2013355 (1995).","journal-title":"Nature"},{"key":"BFni3694_CR44","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1016\/S1074-7613(00)80414-8","volume":"4","author":"T Yoshida","year":"1996","unstructured":"Yoshida, T. et al. Defective B-1 cell development and impaired immunity against Angiostrongylus cantonensis in IL-5R\u03b1-deficient mice. Immunity 4, 483\u2013494 (1996).","journal-title":"Immunity"},{"key":"BFni3694_CR45","doi-asserted-by":"publisher","first-page":"6020","DOI":"10.4049\/jimmunol.172.10.6020","volume":"172","author":"B-g Moon","year":"2004","unstructured":"Moon, B.-g., Takaki, S., Miyake, K. & Takatsu, K. The role of IL-5 for mature B-1 cells in homeostatic proliferation, cell survival, and Ig production. J. Immunol. 172, 6020\u20136029 (2004).","journal-title":"J. Immunol."},{"key":"BFni3694_CR46","doi-asserted-by":"crossref","first-page":"1588","DOI":"10.1182\/blood.V96.4.1588","volume":"96","author":"CL Scott","year":"2000","unstructured":"Scott, C.L. et al. Reassessment of interactions between hematopoietic receptors using common \u03b2-chain and interleukin-3-specific receptor beta-chain-null cells: no evidence of functional interactions with receptors for erythropoietin, granulocyte colony-stimulating factor, or stem cell factor. Blood 96, 1588\u20131590 (2000).","journal-title":"Blood"},{"key":"BFni3694_CR47","doi-asserted-by":"publisher","first-page":"2924","DOI":"10.4049\/jimmunol.164.6.2924","volume":"164","author":"LW Arnold","year":"2000","unstructured":"Arnold, L.W., McCray, S.K., Tatu, C. & Clarke, S.H. Identification of a precursor to phosphatidyl choline-specific B-1 cells suggesting that B-1 cells differentiate from splenic conventional B cells in vivo: cyclosporin A blocks differentiation to B-1. J. Immunol. 164, 2924\u20132930 (2000).","journal-title":"J. Immunol."},{"key":"BFni3694_CR48","doi-asserted-by":"publisher","first-page":"2583","DOI":"10.4049\/jimmunol.1502132","volume":"196","author":"B Guo","year":"2016","unstructured":"Guo, B. & Rothstein, T.L. RasGRP1 Is an essential signaling molecule for development of B1a cells with autoantigen receptors. J. Immunol. 196, 2583\u20132590 (2016).","journal-title":"J. Immunol."},{"key":"BFni3694_CR49","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1002\/eji.200324700","volume":"34","author":"M Seimiya","year":"2004","unstructured":"Seimiya, M. et al. Impaired lymphocyte development and function in Clast5\/Stra13\/DEC1-transgenic mice. Eur. J. Immunol. 34, 1322\u20131332 (2004).","journal-title":"Eur. J. Immunol."},{"key":"BFni3694_CR50","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1038\/nrm1491","volume":"5","author":"DR Hipfner","year":"2004","unstructured":"Hipfner, D.R. & Cohen, S.M. Connecting proliferation and apoptosis in development and disease. Nat. Rev. Mol. Cell Biol. 5, 805\u2013815 (2004).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"BFni3694_CR51","doi-asserted-by":"publisher","first-page":"e2762","DOI":"10.1371\/journal.pone.0002762","volume":"3","author":"MJ Rossner","year":"2008","unstructured":"Rossner, M.J. et al. Disturbed clockwork resetting in Sharp-1 and Sharp-2 single and double mutant mice. PLoS One 3, e2762 (2008).","journal-title":"PLoS One"},{"key":"BFni3694_CR52","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1016\/j.immuni.2008.04.014","volume":"28","author":"K Kwon","year":"2008","unstructured":"Kwon, K. et al. Instructive role of the transcription factor E2A in early B lymphopoiesis and germinal center B cell development. Immunity 28, 751\u2013762 (2008).","journal-title":"Immunity"},{"key":"BFni3694_CR53","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1002\/(SICI)1526-968X(200002)26:2<113::AID-GENE3>3.0.CO;2-2","volume":"26","author":"MD Tallquist","year":"2000","unstructured":"Tallquist, M.D. & Soriano, P. Epiblast-restricted Cre expression in MORE mice: a tool to distinguish embryonic vs. extra-embryonic gene function. Genesis 26, 113\u2013115 (2000).","journal-title":"Genesis"},{"key":"BFni3694_CR54","doi-asserted-by":"publisher","first-page":"197","DOI":"10.4049\/jimmunol.173.1.197","volume":"173","author":"K Kretschmer","year":"2004","unstructured":"Kretschmer, K., Stopkowicz, J., Scheffer, S., Greten, T.F. & Weiss, S. Maintenance of peritoneal B-1a lymphocytes in the absence of the spleen. J. Immunol. 173, 197\u2013204 (2004).","journal-title":"J. Immunol."},{"key":"BFni3694_CR55","doi-asserted-by":"publisher","first-page":"e123","DOI":"10.1093\/nar\/gkp596","volume":"37","author":"D Parkhomchuk","year":"2009","unstructured":"Parkhomchuk, D. et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 37, e123 (2009).","journal-title":"Nucleic Acids Res."},{"key":"BFni3694_CR56","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.immuni.2007.05.019","volume":"27","author":"A Schebesta","year":"2007","unstructured":"Schebesta, A. et al. Transcription factor Pax5 activates the chromatin of key genes involved in B cell signaling, adhesion, migration, and immune function. Immunity 27, 49\u201363 (2007).","journal-title":"Immunity"},{"key":"BFni3694_CR57","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545\u201315550 (2005).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFni3694_CR58","doi-asserted-by":"publisher","first-page":"1728","DOI":"10.1038\/nprot.2012.101","volume":"7","author":"J Feng","year":"2012","unstructured":"Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X.S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728\u20131740 (2012).","journal-title":"Nat. Protoc."},{"key":"BFni3694_CR59","doi-asserted-by":"publisher","first-page":"3130","DOI":"10.1038\/emboj.2012.155","volume":"31","author":"R Revilla-i-Domingo","year":"2012","unstructured":"Revilla-i-Domingo, R. et al. The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis. EMBO J. 31, 3130\u20133146 (2012).","journal-title":"EMBO J."},{"key":"BFni3694_CR60","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"BFni3694_CR61","doi-asserted-by":"publisher","first-page":"3318","DOI":"10.1093\/bioinformatics\/bts607","volume":"28","author":"A Aszodi","year":"2012","unstructured":"Aszodi, A. MULTOVL: fast multiple overlaps of genomic regions. Bioinformatics 28, 3318\u20133319 (2012).","journal-title":"Bioinformatics"},{"key":"BFni3694_CR62","doi-asserted-by":"publisher","first-page":"1696","DOI":"10.1093\/bioinformatics\/btr189","volume":"27","author":"P Machanick","year":"2011","unstructured":"Machanick, P. & Bailey, T.L. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27, 1696\u20131697 (2011).","journal-title":"Bioinformatics"},{"key":"BFni3694_CR63","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","volume":"25","author":"C Trapnell","year":"2009","unstructured":"Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105\u20131111 (2009).","journal-title":"Bioinformatics"},{"key":"BFni3694_CR64","doi-asserted-by":"publisher","first-page":"D662","DOI":"10.1093\/nar\/gku1010","volume":"43","author":"F Cunningham","year":"2015","unstructured":"Cunningham, F. et al. Ensembl 2015. Nucleic Acids Res. 43, D662\u2013D669 (2015).","journal-title":"Nucleic Acids Res."},{"key":"BFni3694_CR65","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","volume":"31","author":"S Anders","year":"2015","unstructured":"Anders, S., Pyl, P.T. & Huber, W. HTSeq\u2013a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166\u2013169 (2015).","journal-title":"Bioinformatics"},{"key":"BFni3694_CR66","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"BFni3694_CR67","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1007\/s12064-012-0162-3","volume":"131","author":"GP Wagner","year":"2012","unstructured":"Wagner, G.P., Kin, K. & Lynch, V.J. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 131, 281\u2013285 (2012).","journal-title":"Theory Biosci."}],"container-title":["Nature Immunology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/ni.3694.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/ni.3694","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/ni.3694.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,22]],"date-time":"2023-08-22T08:39:17Z","timestamp":1692693557000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/ni.3694"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,2,27]]},"references-count":67,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2017,4]]}},"alternative-id":["BFni3694"],"URL":"https:\/\/doi.org\/10.1038\/ni.3694","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.727365389.793548354","asserted-by":"object"},{"id-type":"doi","id":"10.3410\/f.727365389.793530057","asserted-by":"object"}]},"ISSN":["1529-2908","1529-2916"],"issn-type":[{"value":"1529-2908","type":"print"},{"value":"1529-2916","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,2,27]]},"assertion":[{"value":"15 July 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 January 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 February 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}