An epigenetic view of helper T cell differentiation (original) (raw)
Ahmad, K. & Henikoff, S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell9, 1191–1200 (2002). ArticleCASPubMed Google Scholar
Fischle, W., Wang, Y. & Allis, C.D. Histone and chromatin cross-talk. Curr. Opin. Cell Biol.15, 172–183 (2003). ArticleCASPubMed Google Scholar
Bird, A.P. & Wolffe, A.P. Methylation-induced repression: belts, braces, and chromatin. Cell99, 451–454 (1999). ArticleCASPubMed Google Scholar
Tamaru, H. & Selker, E.U. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature414, 277–283 (2001). ArticleCASPubMed Google Scholar
Grogan, J.L. & Locksley, R.M. T helper cell differentiation: on again, off again. Curr. Opin. Immunol.14, 366–372 (2002). ArticleCASPubMed Google Scholar
Murphy, K.M. & Reiner, S.L. The lineage decisions of helper T cells. Nat. Rev. Immunol.2, 933–944 (2002). ArticleCASPubMed Google Scholar
Smale, S.T. & Fisher, A.G. Chromatin structure and gene regulation in the immune system. Annu. Rev. Immunol.20, 427–462 (2002). ArticleCASPubMed Google Scholar
Avni, O. & Rao, A. T cell differentiation: a mechanistic view. Curr. Opin. Immunol.12, 654–659 (2000). ArticleCASPubMed Google Scholar
Glimcher, L.H. & Murphy, K.M. Lineage commitment in the immune system: the T helper lymphocyte grows up. Genes Dev.14, 1693–1711 (2000). CASPubMed Google Scholar
Sad, S. & Mosmann, T.R. Single IL-2-secreting precursor CD4 T cell can develop into either TH1 or TH2 cytokine secretion phenotype. J. Immunol.153, 3514–3522 (1994). CASPubMed Google Scholar
Wang, X. & Mosmann, T. In vivo priming of CD4 T cells that produce interleukin (IL)-2 but not IL-4 or interferon (IFN)-γ, and can subsequently differentiate into IL-4- or IFN-γ-secreting cells. J. Exp. Med.194, 1069–1080 (2001). ArticleCASPubMedPubMed Central Google Scholar
Messi, M. et al. Memory and flexibility of cytokine gene expression as separable properties of human TH1 and TH2 lymphocytes. Nat. Immunol.4, 78–86 (2003). ArticleCASPubMed Google Scholar
Grogan, J.L. et al. Early transcription and silencing of cytokine genes underlie polarization of T helper cell subsets. Immunity14, 205–215 (2001). ArticleCASPubMed Google Scholar
Gross, D.S. & Garrard, W.T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem.57, 159–197 (1988). ArticleCASPubMed Google Scholar
Agarwal, S. & Rao, A. Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation. Immunity9, 765–775 (1998). ArticleCASPubMed Google Scholar
Takemoto, N. et al. TH2-specific DNAse I-hypersensitive sites in the murine IL-13 and IL-4 intergenic region. Int. Immunol.10, 1981–1985 (1998). ArticleCASPubMed Google Scholar
Scotet, E., Schroeder, S. & Lanzavecchia, A. Molecular regulation of CC-chemokine receptor 3 expression in human T helper 2 cells. Blood98, 2568–2570 (2001). ArticleCASPubMed Google Scholar
Hawwari, A., Burrows, J., Vadas, M.A. & Cockerill, P.N. The human IL-3 locus is regulated cooperatively by two NFAT-dependent enhancers that have distinct tissue-specific activities. J. Immunol.169, 1876–1886 (2002). ArticleCASPubMed Google Scholar
Yui, M.A., Hernandez-Hoyos, G. & Rothenberg, E.V. A new regulatory region of the IL-2 locus that confers position-independent transgene expression. J. Immunol.166, 1730–1739 (2001). ArticleCASPubMed Google Scholar
Lee, D.U., Agarwal, S. & Rao, A. TH2 lineage commitment and efficient IL-4 production involves extended demethylation of the IL-4 gene. Immunity16, 649–660 (2002). ArticleCASPubMed Google Scholar
Takemoto, N. et al. Cutting edge: chromatin remodeling at the IL-4/IL-13 intergenic regulatory region for TH2-specific cytokine gene cluster. J. Immunol.165, 6687–6691 (2000). ArticleCASPubMed Google Scholar
Agarwal, S., Avni, O. & Rao, A. Cell-type-restricted binding of the transcription factor NFAT to a distal IL-4 enhancer in vivo. Immunity12, 643–652 (2000). ArticleCASPubMed Google Scholar
Weiss, D.L. & Brown, M.A. Regulation of IL-4 production in mast cells: a paradigm for cell-type-specific gene expression. Immunol. Rev.179, 35–47 (2001). ArticleCASPubMed Google Scholar
Solymar, D.C., Agarwal, S., Bassing, C.H., Alt, F.W. & Rao, A. A 3′ enhancer in the IL-4 gene regulates cytokine production by TH2 cells and mast cells. Immunity17, 41–50 (2002). ArticleCASPubMed Google Scholar
Pennacchio, L.A. & Rubin, E.M. Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet.2, 100–109 (2001). ArticleCASPubMed Google Scholar
Loots, G.G. et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science288, 136–140 (2000). ArticleCASPubMed Google Scholar
Mohrs, M. et al. Deletion of a coordinate regulator of type 2 cytokine expression in mice. Nat. Immunol.2, 842–847 (2001). ArticleCASPubMed Google Scholar
Ellmeier, W., Sunshine, M.J., Losos, K. & Littman, D.R. Multiple developmental stage-specific enhancers regulate CD8 expression in developing thymocytes and in thymus-independent T cells. Immunity9, 485–496 (1998). ArticleCASPubMed Google Scholar
Smith, C.L. & Hager, G.L. Transcriptional regulation of mammalian genes in vivo. A tale of two templates. J. Biol. Chem.272, 27493–27496 (1997). ArticleCASPubMed Google Scholar
Hostert, A. et al. A region in the CD8 gene locus that directs expression to the mature CD8 T cell subset in transgenic mice. Immunity7, 525–536 (1997). ArticleCASPubMed Google Scholar
Lee, G.R., Fields, P.E. & Flavell, R.A. Regulation of IL-4 gene expression by distal regulatory elements and GATA-3 at the chromatin level. Immunity14, 447–459 (2001). ArticleCASPubMed Google Scholar
Killeen, N., Sawada, S. & Littman, D.R. Regulated expression of human CD4 rescues helper T cell development in mice lacking expression of endogenous CD4. EMBO J.12, 1547–1553 (1993). ArticleCASPubMedPubMed Central Google Scholar
Sawada, S., Scarborough, J.D., Killeen, N. & Littman, D.R. A lineage-specific transcriptional silencer regulates CD4 gene expression during T lymphocyte development. Cell77, 917–929 (1994). ArticleCASPubMed Google Scholar
Zou, Y.R. et al. Epigenetic silencing of CD4 in T cells committed to the cytotoxic lineage. Nat. Genet.29, 332–336 (2001). ArticleCASPubMed Google Scholar
Siu, G., Wurster, A.L., Duncan, D.D., Soliman, T.M. & Hedrick, S.M. A transcriptional silencer controls the developmental expression of the CD4 gene. EMBO J.13, 3570–3579 (1994). ArticleCASPubMedPubMed Central Google Scholar
Taniuchi, I., Sunshine, M.J., Festenstein, R. & Littman, D.R. Evidence for distinct CD4 silencer functions at different stages of thymocyte differentiation. Mol. Cell10, 1083–1096 (2002). ArticleCASPubMed Google Scholar
Taniuchi, I. et al. Differential requirements for Runx proteins in CD4 repression and epigenetic silencing during T lymphocyte development. Cell111, 621–633 (2002). ArticleCASPubMed Google Scholar
Avni, O. et al. TH cell differentiation is accompanied by dynamic changes in histone acetylation of cytokine genes. Nat. Immunol.3, 643–651 (2002). ArticleCASPubMed Google Scholar
Fields, P.E., Kim, S.T. & Flavell, R.A. Cutting edge: changes in histone acetylation at the IL-4 and IFN-γ loci accompany TH1/TH2 differentiation. J. Immunol.169, 647–650 (2002). ArticleCASPubMed Google Scholar
Peng, S.L., Gerth, A.J., Ranger, A.M. & Glimcher, L.H. NFATc1 and NFATc2 together control both T and B cell activation and differentiation. Immunity14, 13–20 (2001). ArticleCASPubMed Google Scholar
Ranger, A.M., Oukka, M., Rengarajan, J. & Glimcher, L.H. Inhibitory function of two NFAT family members in lymphoid homeostasis and TH2 development. Immunity9, 627–635 (1998). ArticleCASPubMed Google Scholar
Rengarajan, J., Tang, B. & Glimcher, L.H. NFATc2 and NFATc3 regulate TH2 differentiation and modulate TCR-responsiveness of naive TH cells. Nat. Immunol.3, 48–54 (2002). ArticleCASPubMed Google Scholar
Brogdon, J.L., Leitenberg, D. & Bottomly, K. The potency of TCR signaling differentially regulates NFATc/p activity and early IL-4 transcription in naive CD4+ T cells. J. Immunol.168, 3825–3832 (2002). ArticleCASPubMed Google Scholar
Zhao, K. et al. Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling. Cell95, 625–636 (1999). Article Google Scholar
Shen, X., Xiao, H., Ranallo, R., Wu, W.H. & Wu, C. Modulation of ATP-dependent chromatin-remodeling complexes by inositol polyphosphates. Science299, 112–114 (2003). ArticleCASPubMed Google Scholar
Steger, D.J., Haswell, E.S., Miller, A.L., Wente, S.R. & O'Shea, E.K. Regulation of chromatin remodeling by inositol polyphosphates. Science299, 114–116 (2003). ArticleCASPubMed Google Scholar
Chi, T.H. et al. Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes. Nature418, 195–199 (2002). ArticleCASPubMed Google Scholar
Bird, J.J. et al. Helper T cell differentiation is controlled by the cell cycle. Immunity9, 229–237 (1998). ArticleCASPubMed Google Scholar
Lee, P.P. et al. A critical role for dnmt1 and DNA methylation in T cell development, function, and survival. Immunity15, 763–774 (2001). ArticleCASPubMed Google Scholar
Hutchins, A.S. et al. Gene silencing quantitatively controls the function of a developmental trans-activator. Mol. Cell10, 81–91 (2002). ArticleCASPubMed Google Scholar
Gett, A.V. & Hodgkin, P.D. Cell division regulates the T cell cytokine repertoire, revealing a mechanism underlying immune class regulation. Proc. Natl. Acad. Sci. USA95, 9488–9493 (1998). ArticleCASPubMedPubMed Central Google Scholar
Richter, A., Lohning, M. & Radbruch, A. Instruction for cytokine expression in T helper lymphocytes in relation to proliferation and cell cycle progression. J. Exp. Med.190, 1439–1450 (1999). ArticleCASPubMedPubMed Central Google Scholar
Ben-Sasson, S.Z., Gerstel, R., Hu-Li, J. & Paul, W.E. Cell division is not a “clock” measuring acquisition of competence to produce IFN-γ or IL-4. J. Immunol.166, 112–120 (2001). ArticleCASPubMed Google Scholar
Mullen, A.C. et al. Role of T-bet in commitment of TH1 cells before IL-12-dependent selection. Science292, 1907–1910 (2001). ArticleCASPubMed Google Scholar
Lighvani, A.A. et al. T-bet is rapidly induced by interferon-γ in lymphoid and myeloid cells. Proc. Natl. Acad. Sci. USA98, 15137–15142 (2001). ArticleCASPubMedPubMed Central Google Scholar
Ouyang, W. et al. Stat6-independent GATA-3 autoactivation directs IL-4-independent TH2 development and commitment. Immunity12, 27–37 (2000). ArticleCASPubMed Google Scholar
Szabo, S.J. et al. Distinct effects of T-bet in TH1 lineage commitment and IFN-gamma production in CD4 and CD8 T cells. Science295, 338–342 (2002). ArticleCASPubMed Google Scholar
Mullen, A.C. et al. Hlx is induced by and genetically interacts with T-bet to promote heritable TH1 gene induction. Nat. Immunol.3, 652–658 (2002). ArticleCASPubMed Google Scholar
Afkarian, M. et al. T-bet is a STAT1-induced regulator of IL-12R expression in naive CD4+ T cells. Nat. Immunol.3, 549–557 (2002). ArticleCASPubMed Google Scholar
Szabo, S., Dighe, A., Gubler, U. & Murphy, K. Regulation of the interleukin (IL)-12R b2 subunit expression in developing T helper 1 (TH1) and TH2 cells. J. Exp. Med.185, 817–824 (1997). ArticleCASPubMedPubMed Central Google Scholar
Szabo, S.J. et al. A novel transcription factor, T-bet, directs TH1 lineage commitment. Cell100, 655–669 (2000). ArticleCASPubMed Google Scholar
Ouyang, W. et al. Inhibition of TH1 development mediated by GATA-3 through an IL-4-independent mechanism. Immunity9, 745–755 (1998). ArticleCASPubMed Google Scholar
Lee, H.J. et al. GATA-3 induces T helper cell type 2 (TH2) cytokine expression and chromatin remodeling in committed TH1 cells. J. Exp. Med.192, 105–115 (2000). ArticleCASPubMedPubMed Central Google Scholar
Ho, I.-C., Hodge, M.R., Rooney, J.W. & Glimcher, L.H. The proto-oncogene c-maf is responsible for tissue-specific expression of interleukin-4. Cell85, 973–983 (1996). ArticleCASPubMed Google Scholar
Asnagli, H., Afkarian, M. & Murphy, K.M. Cutting edge: identification of an alternative GATA-3 promoter directing tissue-specific gene expression in mouse and human. J. Immunol.168, 4268–4271 (2002). ArticleCASPubMed Google Scholar
Kurata, H. et al. Friend of GATA is expressed in naive TH cells and functions as a repressor of GATA-3-mediated TH2 cell development. J. Immunol.168, 4538–4545 (2002). ArticleCASPubMed Google Scholar
Miaw, S.C., Choi, A., Yu, E., Kishikawa, H. & Ho, I.C. ROG, repressor of GATA, regulates the expression of cytokine genes. Immunity12, 323–333 (2000). ArticleCASPubMed Google Scholar
Kelly, B.L. & Locksley, R.M. Coordinate regulation of the IL-4, IL-13, and IL-5 cytokine cluster in TH2 clones revealed by allelic expression patterns. J. Immunol.165, 2982–2986 (2000). ArticleCASPubMed Google Scholar
Cousins, D.J., Lee, T.H. & Staynov, D.Z. Cytokine coexpression during human TH1/TH2 cell differentiation: direct evidence for coordinated expression of TH2 cytokines. J. Immunol.169, 2498–2506 (2002). ArticleCASPubMed Google Scholar
Cohen, B.A., Mitra, R.D., Hughes, J.D. & Church, G.M. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat. Genet.26, 183–186 (2000). ArticleCASPubMed Google Scholar
Boutanaev, A.M., Kalmykova, A.I., Shevelyov, Y.Y. & Nurminsky, D.I. Large clusters of co-expressed genes in the Drosophila genome. Nature420, 666–669 (2002). ArticleCASPubMed Google Scholar
Fransz, P., De Jong, J.H., Lysak, M., Castiglione, M.R. & Schubert, I. Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc. Natl. Acad. Sci. USA99, 14584–14589 (2002). ArticleCASPubMedPubMed Central Google Scholar
Yamashita, M. et al. Identification of a conserved GATA3 response element upstream proximal from the interleukin-13 gene locus. J. Biol. Chem.277, 42399–42408 (2002). ArticleCASPubMed Google Scholar
Noma, K., Allis, C.D. & Grewal, S.I. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science293, 1150–1155 (2001). ArticleCASPubMed Google Scholar
Litt, M.D., Simpson, M., Gaszner, M., Allis, C.D. & Felsenfeld, G. Correlation between histone lysine methylation and developmental changes at the chicken β-globin locus. Science293, 2453–2455 (2001). ArticleCASPubMed Google Scholar
Adlam, M. & Siu, G. Hierarchical interactions control CD4 gene expression during thymocyte development. Immunity18, 173–184 (2003). ArticleCASPubMed Google Scholar
Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F. & de Laat, W. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol. Cell10, 1453–1465 (2002). ArticleCASPubMed Google Scholar
Carter, D., Chakalova, L., Osborne, C.S., Dai, Y.F. & Fraser, P. Long-range chromatin regulatory interactions in vivo. Nat. Genet.32, 623–626 (2002). ArticleCASPubMed Google Scholar
Kosak, S.T. et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science296, 158–162 (2002). ArticleCASPubMed Google Scholar
Schebesta, M., Heavey, B. & Busslinger, M. Transcriptional control of B-cell development. Curr. Opin. Immunol.14, 216–223 (2002). ArticleCASPubMed Google Scholar
Horcher, M., Souabni, A. & Busslinger, M. Pax5/BSAP maintains the identity of B cells in late B lymphopoiesis. Immunity14, 779–790 (2001). ArticleCASPubMed Google Scholar
Guo, L. et al. In TH2 cells the Il4 gene has a series of accessibility states associated with distinctive probabilities of IL-4 production. Proc. Natl. Acad. Sci. USA99, 10623–10628 (2002). ArticleCASPubMedPubMed Central Google Scholar
Zhang, J., Xu, F., Hashimshony, T., Keshet, I. & Cedar, H. Establishment of transcriptional competence in early and late S phase. Nature420, 198–202 (2002). ArticleCASPubMed Google Scholar
Rogan, D.F., Cousins, D.J. & Staynov, D.Z. Intergenic transcription occurs throughout the human IL-4/IL-13 gene cluster. Biochem. Biophys. Res. Commun.255, 556–561 (1999). ArticleCASPubMed Google Scholar
Cohen, D.E. & Lee, J.T. X-chromosome inactivation and the search for chromosome-wide silencers. Curr. Opin. Genet. Dev.12, 219–224 (2002). ArticleCASPubMed Google Scholar
Hall, I.M. et al. Establishment and maintenance of a heterochromatin domain. Science297, 2232–2237 (2002). ArticleCASPubMed Google Scholar
Czermin, B. et al. Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell111, 185–196 (2002). ArticleCASPubMed Google Scholar
Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science298, 1039–1043 (2002). ArticleCASPubMed Google Scholar
Muller, J. et al. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell111, 197–208 (2002). ArticleCASPubMed Google Scholar
Kimura, M. et al. Regulation of TH2 cell differentiation by mel-18, a mammalian polycomb group gene. Immunity15, 275–287 (2001). ArticleCASPubMed Google Scholar
Sweetser, M.T. et al. The roles of nuclear factor of activated T cells and yin-yang 1 in activation-induced expression of the interferon-γ promoter in T cells. J. Biol. Chem.273, 34775–34783 (1998). ArticleCASPubMed Google Scholar
Guo, J. et al. Yin-Yang 1 activates interleukin-4 gene expression in T cells. J. Biol. Chem.276, 48871–48878 (2001). ArticleCASPubMed Google Scholar
Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature410, 116–120 (2001). ArticleCASPubMed Google Scholar
Bannister, A.J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature410, 120–124 (2001). ArticleCASPubMed Google Scholar
Festenstein, R. et al. Modulation of heterochromatin protein 1 dynamics in primary Mammalian cells. Science299, 719–721 (2003). ArticleCASPubMed Google Scholar