Ahmed, R. & Gray, D. Immunological memory and protective immunity: understanding their relation. Science 272, 54–60 (1996).
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, 281–295 (2007).
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, 1191–1198 (2003).
Zhou, X. et al. Differentiation and persistence of memory CD8+ T cells depend on T cell factor 1. Immunity 33, 229–240 (2010).
Chang, J.T., Wherry, E.J. & Goldrath, A.W. Molecular regulation of effector and memory T cell differentiation. Nat. Rev. Immunol. 15, 1104–1115 (2014).
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, 1213–1218 (2013).
Winter, D. et al. Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape. Nat. Rev. Immunol. 15, 585–594 (2015).
Neph, S. et al. Circuitry and dynamics of human transcription factor regulatory networks. Cell 150, 1274–1286 (2010).
Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116–120 (2012).
Spitz, F. & Furlong, E.E.M. Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet. 13, 613–626 (2012).
Calo, E. & Wysocka, J. Modification of enhancer chromatin: what, how, and why? Mol. Cell 49, 825–837 (2013).
Lara-Astiaso, D. et al. Chromatin state dynamics during blood formation. Science 345, 943–949 (2014).
Lavin, Y. et al. Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. Cell 159, 1312–1326 (2014).
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, 912–925 (2009).
Russ, B.E. et al. Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8+ T cell differentiation. Immunity 41, 853–865 (2014).
Heintzman, N.D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).
Best, J.A. et al. Transcriptional insights into the CD8+ T cell response to infection and memory T cell formation. Nat. Immunol. 29, 997–1003 (2013).
Rubinstein, M. et al. IL-7 and IL-15 differentially regulate CD8+ T-cell subsets during contraction of the immune response. Blood 112, 3704–3712 (2008).
Yang, C.Y. et al. The transcriptional regulators Id2 and Id3 control the formation of distinct memory CD8+ T cell subsets. Nat. Immunol. 12, 1221–1229 (2011).
Miyazaki, M. et al. The opposing roles of E2A and Id3 that orchestrate and enforce the naïve T cell fate. Nat. Immunol. 12, 992–1001 (2012).
Rajagopal, N. et al. RFECS: A random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput. Biol. 9, e1002968 (2013).
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, 1013–1016 (2014).
McLean, C.Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495–501 (2010).
Ma, C. & Zhang, N. Transforming growth factor-β signaling is constantly shaping memory T-cell population. Proc. Natl. Acad. Sci. USA 112, 11013–11017 (2015).
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, 2027–2039 (2015).
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, 2041–2056 (2015).
Intlekofer, A.M. et al. Effector and memory CD8+ T cell fate coupled by T-bet and eomesodermin. Nat. Immunol. 6, 1236–1244 (2005).
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, 489–499 (2013).
Kurachi, M. et al. The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells. Nat. Immunol. 15, 373–383 (2014).
Zhou, X. & Xue, H. Generation of memory precursors and functional memory CD8+ T cells depends on TCF-1 and LEF-1. J. Immunol. 189, 2722–2726 (2012).
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, 2031–2041 (2012).
Rincón, 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, 4370–4381 (1994).
Doering, T. et al. Network analysis reveals centrally connected genes and pathways involved in CD8+ T Cell exhaustion versus memory. Immunity 37, 1130–1144 (2012).
Hu, G. & Chen, J. A genome-wide regulatory network identifies key transcription factors for memory CD8+ T-cell development. Nat. Commun. 4, 2830 (2013).
Szabo, S.J. et al. Distinct effects of T-bet in TH1 lineage commitment and IFN-γ production in CD4 and CD8 T cells. Science 295, 338–342 (2002).
Lord, G.M. et al. T-bet is required for optimal proinflammatory CD4+ T-cell trafficking. Blood 106, 3432–3439 (2005).
Page, L., Brin, S., Motwani, R. & Winograd, T. The PageRank citation ranking: bringing order to the web. World Wide Web (Bussum) 54, 1–17 (1998).
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, 792–805 (2011).
Arrieta-Ortiz, M.L. et al. An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network. Mol. Syst. Biol. 11, 839 (2015).
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).
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, 276–281 (2013).
Liu, H. et al. Yin Yang 1 is a critical regulator of B-cell development. Genes Dev. 21, 1179–1189 (2007).
Herold, M.J., McPherson, K.G. & Reichardt, H.M. Glucocorticoids in T cell apoptosis and function. Cell. Mol. Life Sci. 63, 60–72 (2006).
Franchimont, D. et al. Positive effects of glucocorticoids on T cell function by up-regulation of IL-7 receptor alpha. J. Immunol. 168, 2212–2218 (2002).
Smoak, K.A. & Cidlowski, J.A. Mechanisms of glucocorticoid receptor signaling during inflammation. Mech. Ageing Dev. 125, 697–706 (2004).
Wang, Q. et al. Equilibrium interactions of corepressors and coactivators with agonist and antagonist complexes of glucocorticoid receptors. Mol. Endocrinol. 18, 1376–1395 (2004).
Tsankov, A.M. et al. Transcription factor binding dynamics during human ES cell differentiation. Nature 518, 344–349 (2015).
Zhang, K., Li, N., Ainsworth, R. & Wang, W. Systematic identification of protein combinations mediating chromatin looping. Nat. Commun. 7, 1–11 (2016).
Dixon, J.R. et al. Chromatin architecture reorganization during stem cell differentiation. Nature 518, 331–336 (2015).
Zhu, Y. et al. Constructing 3D interaction maps from 1D epigenomes. Nat. Commun. 7, 10812 (2016).
Chen, R. et al. In vivo RNA interference screens identify regulators of antiviral CD4+ and CD8+ T cell differentiation. Immunity 41, 325–338 (2014).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Zhang, Y. et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
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–D115 (2016).
Newburger, D.E. & Bulyk, M.L. UniPROBE: An online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res. 37, 77–82 (2009).
Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327–339 (2013).
Grant, C.E., Bailey, T.L. & Noble, W.S. FIMO: Scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011).
Jeh, G. & Widom, J. Scaling personalized web search. Proc. 2003 Int. World Wide Web Conf. (WWW'03) 12, 271–279 (2003).