Deletion of a conserved Il4 silencer impairs T helper type 1–mediated immunity (original) (raw)

• Murphy, K.M. & Reiner, S.L. The lineage decisions of helper T cells. Nat. Rev. Immunol. 2, 933–944 (2002).
  Article CAS PubMed Google Scholar
• Ansel, K.M., Lee, D.U. & Rao, A. An epigenetic view of helper T cell differentiation. Nat. Immunol. 4, 616–623 (2003).
  Article CAS PubMed Google Scholar
• Szabo, S.J. et al. A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell 100, 655–669 (2000).
  Article CAS PubMed Google Scholar
• Szabo, S.J., Sullivan, B.M., Peng, S.L. & Glimcher, L.H. Molecular mechanisms regulating Th1 immune responses. Annu Rev. Immunol. 21, 713–758 (2003).
  Article CAS PubMed Google Scholar
• Pai, S.Y., Truitt, M.L. & Ho, I.C. GATA-3 deficiency abrogates the development and maintenance of T helper type 2 cells. Proc. Natl. Acad. Sci. USA 101, 1993–1998 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Grogan, J.L. & Locksley, R.M. T helper cell differentiation: on again, off again. Curr. Opin. Immunol. 14, 366–372 (2002).
  CAS PubMed 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. Immunity 16, 649–660 (2002).
  Article CAS PubMed Google Scholar
• Grogan, J.L. et al. Basal chromatin modification at the IL-4 gene in helper T cells. J. Immunol. 171, 6672–6679 (2003).
  Article CAS PubMed Google Scholar
• Baguet, A. & Bix, M. Chromatin landscape dynamics of the Il4-Il13 locus during T helper 1 and 2 development. Proc. Natl. Acad. Sci. USA 101, 11410–11415 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Grogan, J.L. et al. Early transcription and silencing of cytokine genes underlie polarization of T helper cell subsets. Immunity 14, 205–215 (2001).
  Article CAS PubMed 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).
  Article CAS PubMed 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).
  Article CAS PubMed 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).
  CAS PubMed Google Scholar
• Ouyang, W. et al. Inhibition of Th1 development mediated by GATA-3 through an IL-4-independent mechanism. Immunity 9, 745–755 (1998).
  Article CAS PubMed Google Scholar
• Levine, M. & Tjian, R. Transcription regulation and animal diversity. Nature 424, 147–151 (2003).
  Article CAS PubMed Google Scholar
• Frazer, K.A., Elnitski, L., Church, D.M., Dubchak, I. & Hardison, R.C. Cross-species sequence comparisons: a review of methods and available resources. Genome Res. 13, 1–12 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Nardone, J., Lee, D.U., Ansel, K.M. & Rao, A. Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA. Nat. Immunol. 5, 768–774 (2004).
  Article CAS PubMed Google Scholar
• Loots, G.G. et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288, 136–140 (2000).
  Article CAS PubMed Google Scholar
• Agarwal, S. & Rao, A. Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation. Immunity 9, 765–775 (1998).
  Article CAS PubMed 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).
  Article CAS PubMed 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. Immunity 14, 447–459 (2001).
  Article CAS PubMed Google Scholar
• Lee, G.R., Fields, P.E., Griffin, T.J. & Flavell, R.A. Regulation of the Th2 cytokine locus by a locus control region. Immunity 19, 145–153 (2003).
  Article CAS PubMed Google Scholar
• Mohrs, M. et al. Deletion of a coordinate regulator of type 2 cytokine expression in mice. Nat. Immunol. 2, 842–847 (2001).
  Article CAS PubMed 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. Immunity 17, 41–50 (2002).
  Article CAS PubMed Google Scholar
• Lee, D.U. & Rao, A. Molecular analysis of a locus control region in the Th2 cytokine gene cluster. Proc. Natl. Acad. Sci. USA (in the press).
• Spilianakis, C.G. & Flavell, R.A. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat. Immunol. 5, 1017–1027 (2004).
  Article CAS PubMed 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. Immunity 12, 643–652 (2000).
  Article CAS PubMed Google Scholar
• Dubchak, I. et al. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 10, 1304–1306 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Schneider, R. et al. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat. Cell Biol. 6, 73–77 (2004).
  Article CAS PubMed Google Scholar
• Morshead, K.B., Ciccone, D.N., Taverna, S.D., Allis, C.D. & Oettinger, M.A. Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4. Proc. Natl. Acad. Sci. USA 100, 11577–11582 (2003).
  Article CAS PubMed PubMed Central 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).
  Article CAS PubMed Google Scholar
• Monticelli, S., Solymar, D.C. & Rao, A. Role of NFAT proteins in IL13 gene transcription in mast cells. J. Biol. Chem. 279, 36210–36218 (2004).
  Article CAS PubMed Google Scholar
• Kubo, M. et al. T-cell subset-specific expression of the IL-4 gene is regulated by a silencer element and STAT6. EMBO J. 16, 4007–4020 (1997).
  Article CAS PubMed PubMed 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).
  Article CAS PubMed Google Scholar
• Makar, K.W. & Wilson, C.B. DNA methylation is a nonredundant repressor of the Th2 effector program. J. Immunol. 173, 4402–4406 (2004).
  Article CAS PubMed Google Scholar
• Hutchins, A.S. et al. Gene silencing quantitatively controls the function of a developmental trans-activator. Mol. Cell 10, 81–91 (2002).
  Article CAS PubMed Google Scholar
• Feng, Q. & Zhang, Y. The MeCP1 complex represses transcription through preferential binding, remodeling, and deacetylating methylated nucleosomes. Genes Dev. 15, 827–832 (2001).
  CAS PubMed PubMed Central 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).
  Article CAS PubMed Google Scholar
• Crawford, G.E. et al. Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. Proc. Natl. Acad. Sci. USA 101, 992–997 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Im, S.H., Hueber, A., Monticelli, S., Kang, K.H. & Rao, A. Chromatin-level regulation of the IL10 gene in T cells. J. Biol. Chem. 279, 46818–46825 (2004).
  Article CAS PubMed Google Scholar
• Yannoutsos, N. et al. A cis element in the recombination activating gene locus regulates gene expression by counteracting a distant silencer. Nat. Immunol. 5, 443–450 (2004).
  Article CAS PubMed 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. Cell 77, 917–929 (1994).
  Article CAS PubMed 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).
  Article CAS PubMed Google Scholar
• Su, R.C. et al. Dynamic assembly of silent chromatin during thymocyte maturation. Nat. Genet. 36, 502–506 (2004).
  Article CAS PubMed Google Scholar
• Sacks, D. & Noben-Trauth, N. The immunology of susceptibility and resistance to Leishmania major in mice. Nat. Rev. Immunol. 2, 845–858 (2002).
  Article CAS PubMed Google Scholar
• Wang, Z.E., Reiner, S.L., Zheng, S., Dalton, D.K. & Locksley, R.M. CD4+ effector cells default to the Th2 pathway in interferon-γ-deficient mice infected with Leishmania major. J. Exp. Med. 179, 1367–1371 (1994).
  Article CAS PubMed Google Scholar
• Gorman, J.R. et al. The Igκ enhancer influences the ratio of Igκ versus Igλ B lymphocytes. Immunity 5, 241–252 (1996).
  Article CAS PubMed Google Scholar
• Brown, J.A. et al. T helper differentiation in resistant and susceptible B7-deficient mice infected with Leishmania major. Eur. J. Immunol. 32, 1764–1772 (2002).
  Article CAS PubMed Google Scholar
• Frazer, K.A., Pachter, L., Poliakov, A., Rubin, E.M. & Dubchak, I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 32, W273–279 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Satoskar, A., Okano, M. & David, J.R. Gammadelta T cells are not essential for control of cutaneous Leishmania major infection in genetically resistant C57BL/6 mice. J. Infect. Dis. 176, 1649–1652 (1997).
  Article CAS PubMed Google Scholar