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Dynamic changes in histone-methylation 'marks' across the locus encoding interferon-γ during the differentiation of T helper type 2 cells

Nature Immunology volume 8, pages 723–731 (2007)Cite this article

Abstract

The 'histone-code' hypothesis proposes that cell fate 'decisions' are achieved through the creation of stable epigenetic histone 'marks' at gene loci. Here we explored the formation of marks of repressive methylation of histone 3 at lysine 9 (H3-K9) and of H3-K27 at the locus encoding interferon-γ (Ifng locus) during the commitment of naive T cells to the T helper type 1 (TH1) and TH2 lineages. Methylation of H3-K9 across the Ifng locus was rapidly induced in differentiating TH1 and TH2 cells and was sustained in TH1 cells. In contrast, TH2 differentiation caused loss of methylation of H3-K9 and gain of methylation of H3-K27 by mechanisms dependent on the transcription factors GATA-3 and STAT6. Thus, histone-methylation marks at the Ifng locus are highly dynamic, which may ensure higher-order transcriptional regulation during early lineage commitment.

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Figure 1: H3-K9- and H3-K27-methylation status of the Ifng, Il4 and Il2 promoters in effector TH2 cells.
Figure 2: Dynamic alterations in the status of histone methylation across the Ifng locus in developing TH2 cells.
Figure 3: H3-K9- and H3-K27-methylation status across the Ifng locus in developing TH1 cells.
Figure 4: Trimethylation of H3-K27 across the Ifng locus.
Figure 5: Methylation of H3-K9 and H3-K27 across the Ifng locus in fibroblasts.
Figure 6: STAT6 and GATA-3 bind to the Ifng locus in vivo.
Figure 7: Lack of STAT6 reverses the histone-methylation status of the Ifng locus and creates a favorable transcriptional environment.
Figure 8: GATA-3 induces dimethylation of H3-K27 and recruitment of EZH2 to the Ifng locus in effector TH1 cells and inhibits Ifng transcription.

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References

  1. vanHolde, K.E. Chromatin (Springer Verlag, New York, 1988).

  2. Berger, S.L. Histone modifications in transcriptional regulation. Curr. Opin. Genet. Dev. 12, 142–148 (2002).

    Article  CAS  Google Scholar 

  3. Margueron, R., Trojer, P. & Reinberg, D. The key to development: interpreting the histone code? Curr. Opin. Genet. Dev. 15, 163–176 (2005).

    Article  CAS  Google Scholar 

  4. Vakoc, C.R., Mandat, S.A., Olenchock, B.A. & Blobel, G.A. Histone H3 lysine 9 methylation and HP1γ are associated with transcription elongation through mammalian chromatin. Mol. Cell 19, 381–391 (2005).

    Article  CAS  Google Scholar 

  5. Santos-Rosa, H. et al. Active genes are tri-methylated at K4 of histone H3. Nature 419, 407–411 (2002).

    Article  CAS  Google Scholar 

  6. Bernstein, B.E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).

    Article  CAS  Google Scholar 

  7. Lindroth, A.M. et al. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J. 23, 4286–4296 (2004).

    Article  CAS  Google Scholar 

  8. Dutnall, R.N. Cracking the histone code: one, two, three methyls, you're out!. Mol. Cell 12, 3–4 (2003).

    Article  CAS  Google Scholar 

  9. Turner, B.M. Cellular memory and the histone code. Cell 111, 285–291 (2002).

    Article  CAS  Google Scholar 

  10. Strahl, B.D. & Allis, C.D. The language of covalent histone modifications. Nature 403, 41–45 (2000).

    Article  CAS  Google Scholar 

  11. Zhou, W., Chang, S. & Aune, T.M. Long-range histone acetylation of the Ifng gene is an essential feature of T cell differentiation. Proc. Natl. Acad. Sci. USA 101, 2440–2445 (2004).

    Article  CAS  Google Scholar 

  12. Chang, S. & Aune, T.M. Histone hyperacetylated domains across the Ifng gene region in natural killer cells and T cells. Proc. Natl. Acad. Sci. USA 102, 17095–17100 (2005).

    Article  CAS  Google Scholar 

  13. Forsberg, E.C. et al. Developmentally dynamic histone acetylation pattern of a tissue-specific chromatin domain. Proc. Natl. Acad. Sci. USA 97, 14494–14499 (2000).

    Article  CAS  Google Scholar 

  14. Su, R.C. et al. Dynamic assembly of silent chromatin during thymocyte maturation. Nat. Genet. 36, 502–506 (2004).

    Article  CAS  Google Scholar 

  15. Calestagne-Morelli, A. & Ausio, J. Long-range histone acetylation: biological significance, structural implications, and mechanisms. Biochem. Cell Biol. 84, 518–527 (2006).

    Article  CAS  Google Scholar 

  16. Papp, B. & Muller, J. Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. Genes Dev. 20, 2041–2054 (2006).

    Article  CAS  Google Scholar 

  17. Eivazova, E.R. & Aune, T.M. Dynamic alterations in the conformation of the Ifng gene region during T helper cell differentiation. Proc. Natl. Acad. Sci. USA 101, 251–256 (2004).

    Article  CAS  Google Scholar 

  18. Kahn, T.G., Schwartz, Y.B., Dellino, G.I. & Pirrotta, V. Polycomb complexes and the propagation of the methylation mark at the Drosophila ubx gene. J. Biol. Chem. 281, 29064–29075 (2006).

    Article  CAS  Google Scholar 

  19. Forsberg, E.C. & Bresnick, E.H. Histone acetylation beyond promoters: long-range acetylation patterns in the chromatin world. Bioessays 23, 820–830 (2001).

    Article  CAS  Google Scholar 

  20. Ansel, K.M., Lee, D.U. & Rao, A. An epigenetic view of helper T cell differentiation. Nat. Immunol. 4, 616–623 (2003).

    Article  CAS  Google Scholar 

  21. Lee, G.R., Kim, S.T., Spilianakis, C.G., Fields, P.E. & Flavell, R.A. T helper cell differentiation: regulation by cis elements and epigenetics. Immunity 24, 369–379 (2006).

    Article  CAS  Google Scholar 

  22. 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  Google Scholar 

  23. Wilson, C.B. & Merkenschlager, M. Chromatin structure and gene regulation in T cell development and function. Curr. Opin. Immunol. 18, 143–151 (2006).

    Article  CAS  Google Scholar 

  24. 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  Google Scholar 

  25. Szabo, S.J. et al. A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell 100, 655–669 (2000).

    Article  CAS  Google Scholar 

  26. Zheng, W. & Flavell, R.A. The transcription factor GATA-3 is necessary and sufficient for Th2 cytokine gene expression in CD4 T cells. Cell 89, 587–596 (1997).

    Article  CAS  Google Scholar 

  27. Thierfelder, W.E. et al. Requirement for Stat4 in interleukin-12-mediated responses of natural killer and T cells. Nature 382, 171–174 (1996).

    Article  CAS  Google Scholar 

  28. 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  Google Scholar 

  29. Agarwal, S. & Rao, A. Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation. Immunity 9, 765–775 (1998).

    Article  CAS  Google Scholar 

  30. 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  Google Scholar 

  31. 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  Google Scholar 

  32. 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  Google Scholar 

  33. Schubert, D. et al. Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27. EMBO J. 25, 4638–4649 (2006).

    Article  CAS  Google Scholar 

  34. Mohd-Sarip, A. et al. Architecture of a polycomb nucleoprotein complex. Mol. Cell 24, 91–100 (2006).

    Article  CAS  Google Scholar 

  35. Ringrose, L., Ehret, H. & Paro, R. Distinct contributions of histone H3 lysine 9 and 27 methylation to locus-specific stability of polycomb complexes. Mol. Cell 16, 641–653 (2004).

    Article  CAS  Google Scholar 

  36. Felsenstein, J. & Churchill, G.A. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13, 93–104 (1996).

    Article  CAS  Google Scholar 

  37. Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005).

    Article  CAS  Google Scholar 

  38. Xu, X., Sun, Y.L. & Hoey, T. Cooperative DNA binding and sequence-selective recognition conferred by the STAT amino-terminal domain. Science 273, 794–797 (1996).

    Article  CAS  Google Scholar 

  39. Laible, G. et al. Mammalian homologues of the Polycomb-group gene Enhancer of zeste mediate gene silencing in Drosophila heterochromatin and at S. cerevisiae telomeres. EMBO J. 16, 3219–3232 (1997).

    Article  CAS  Google Scholar 

  40. Ringrose, L. & Paro, R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38, 413–443 (2004).

    Article  CAS  Google Scholar 

  41. Yao, Y.L., Yang, W.M. & Seto, E. Regulation of transcription factor YY1 by acetylation and deacetylation. Mol. Cell. Biol. 21, 5979–5991 (2001).

    Article  CAS  Google Scholar 

  42. Caretti, G., Di Padova, M., Micales, B., Lyons, G.E. & Sartorelli, V. The Polycomb Ezh2 methyltransferase regulates muscle gene expression and skeletal muscle differentiation. Genes Dev. 18, 2627–2638 (2004).

    Article  CAS  Google Scholar 

  43. Soutto, M. et al. A minimal IFN-gamma promoter confers Th1 selective expression. J. Immunol. 169, 4205–4212 (2002).

    Article  CAS  Google Scholar 

  44. Ye, J., Cippitelli, M., Dorman, L., Ortaldo, J.R. & Young, H.A. The nuclear factor YY1 suppresses the human γ interferon promoter through two mechanisms: inhibition of AP1 binding and activation of a silencer element. Mol. Cell. Biol. 16, 4744–4753 (1996).

    Article  CAS  Google Scholar 

  45. Usui, T. et al. T-bet regulates Th1 responses through essential effects on GATA-3 function rather than on IFNG gene acetylation and transcription. J. Exp. Med. 203, 755–766 (2006).

    Article  CAS  Google Scholar 

  46. Hwang, E.S., Szabo, S.J., Schwartzberg, P.L. & Glimcher, L.H. T helper cell fate specified by kinase-mediated interaction of T-bet with GATA-3. Science 307, 430–433 (2005).

    Article  CAS  Google Scholar 

  47. Koyanagi, M. et al. EZH2 and histone 3 trimethyl lysine 27 associated with Il4 and Il13 gene silencing in Th1 cells. J. Biol. Chem. 280, 31470–31477 (2005).

    Article  CAS  Google Scholar 

  48. Dermitzakis, E.T., Reymond, A. & Antonarakis, S.E. Conserved non-genic sequences - an unexpected feature of mammalian genomes. Nat. Rev. Genet. 6, 151–157 (2005).

    Article  CAS  Google Scholar 

  49. Hatton, R.D. et al. A distal conserved sequence element controls Ifng gene expression by T cells and NK cells. Immunity 25, 717–729 (2006).

    Article  CAS  Google Scholar 

  50. Rodriguez-Galan, M.C., Bream, J.H., Farr, A. & Young, H.A. Synergistic effect of IL-2, IL-12, and IL-18 on thymocyte apoptosis and Th1/Th2 cytokine expression. J. Immunol. 174, 2796–2804 (2005).

    Article  CAS  Google Scholar 

  51. Lee, D.U., Avni, O., Chen, L. & Rao, A. A distal enhancer in the interferon-γ (IFN-γ) locus revealed by genome sequence comparison. J. Biol. Chem. 279, 4802–4810 (2004).

    Article  CAS  Google Scholar 

  52. Shnyreva, M. et al. Evolutionarily conserved sequence elements that positively regulate IFN-γ expression in T cells. Proc. Natl. Acad. Sci. USA 101, 12622–12627 (2004).

    Article  CAS  Google Scholar 

  53. Soutto, M., Zhou, W. & Aune, T.M. Cutting edge: distal regulatory elements are required to achieve selective expression of IFN-γ in Th1/Tc1 effector cells. J. Immunol. 169, 6664–6667 (2002).

    Article  CAS  Google Scholar 

  54. 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  Google Scholar 

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Acknowledgements

We thank E.M. Oltz for comments and review of the manuscript. Supported by the National Institutes of Health (AI 44924).

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Authors and Affiliations

  1. Division of Rheumatology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, 37232, Tennessee, USA

    Shaojing Chang & Thomas M Aune

  2. Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, 37232, Tennessee, USA

    Thomas M Aune

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  1. Shaojing Chang
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Contributions

S.C. and T.M.A. contributed to discussions, experimental design, data analysis, execution of experiments and preparation of the manuscript.

Note: Supplementary information is available on the Nature Immunology website.

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Correspondence to Thomas M Aune.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Kinetics of Ifng mRNA and IFN-γ protein expression following T cell stimulation. (PDF 269 kb)

Supplementary Fig. 2

EZH2 recruitment to the Ifng locus in developing TH1 and TH2 cells. (PDF 251 kb)

Supplementary Table 1

Primer sequences used for ChIP analysis. (PDF 48 kb)

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Chang, S., Aune, T. Dynamic changes in histone-methylation 'marks' across the locus encoding interferon-γ during the differentiation of T helper type 2 cells. Nat Immunol 8, 723–731 (2007). https://doi.org/10.1038/ni1473

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