Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate (original) (raw)

Nature volume 463, pages 808–812 (2010)Cite this article

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Abstract

Immune homeostasis is dependent on tight control over the size of a population of regulatory T (Treg) cells capable of suppressing over-exuberant immune responses. The Treg cell subset is comprised of cells that commit to the Treg lineage by upregulating the transcription factor Foxp3 either in the thymus (tTreg) or in the periphery (iTreg)1,2. Considering a central role for Foxp3 in Treg cell differentiation and function3,4, we proposed that conserved non-coding DNA sequence (CNS) elements at the Foxp3 locus encode information defining the size, composition and stability of the Treg cell population. Here we describe the function of three Foxp3 CNS elements (CNS1–3) in Treg cell fate determination in mice. The pioneer element CNS3, which acts to potently increase the frequency of Treg cells generated in the thymus and the periphery, binds c-Rel in in vitro assays. In contrast, CNS1, which contains a TGF-β–NFAT response element, is superfluous for tTreg cell differentiation, but has a prominent role in iTreg cell generation in gut-associated lymphoid tissues. CNS2, although dispensable for Foxp3 induction, is required for Foxp3 expression in the progeny of dividing Treg cells. Foxp3 binds to CNS2 in a Cbf-β–Runx1 and CpG DNA demethylation-dependent manner, suggesting that Foxp3 recruitment to this ‘cellular memory module’ facilitates the heritable maintenance of the active state of the Foxp3 locus and, therefore, Treg lineage stability. Together, our studies demonstrate that the composition, size and maintenance of the Treg cell population are controlled by Foxp3 CNS elements engaged in response to distinct cell-extrinsic or -intrinsic cues.

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References

  1. Sakaguchi, S., Yamaguchi, T., Nomura, T. & Ono, M. Regulatory T cells and immune tolerance. Cell 133, 775–787 (2008)
    Article CAS Google Scholar
  2. Zheng, Y. & Rudensky, A. Y. Foxp3 in control of the regulatory T cell lineage. Nature Immunol. 8, 457–462 (2007)
    Article CAS Google Scholar
  3. Gavin, M. A. et al. Foxp3-dependent programme of regulatory T-cell differentiation. Nature 445, 771–775 (2007)
    Article ADS CAS Google Scholar
  4. Williams, L. M. & Rudensky, A. Y. Maintenance of the Foxp3-dependent developmental program in mature regulatory T cells requires continued expression of Foxp3. Nature Immunol. 8, 277–284 (2007)
    Article CAS Google Scholar
  5. Ruthenburg, A. J., Allis, C. D. & Wysocka, J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell 25, 15–30 (2007)
    Article CAS Google Scholar
  6. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007)
    Article ADS CAS Google Scholar
  7. Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genet. 39, 311–318 (2007)
    Article CAS Google Scholar
  8. Tone, Y. et al. Smad3 and NFAT cooperate to induce Foxp3 expression through its enhancer. Nature Immunol. 9, 194–202 (2007)
    Article Google Scholar
  9. Kim, H. P. & Leonard, W. J. CREB/ATF-dependent T cell receptor-induced FoxP3 gene expression: a role for DNA methylation. J. Exp. Med. 204, 1543–1551 (2007)
    Article CAS Google Scholar
  10. Burchill, M. A., Yang, J., Vogtenhuber, C., Blazar, B. R. & Farrar, M. A. IL-2 receptor β-dependent STAT5 activation is required for the development of Foxp3+ regulatory T cells. J. Immunol. 178, 280–290 (2007)
    Article CAS Google Scholar
  11. Rao, S., Gerondakis, S., Woltring, D. & Shannon, M. F. c-Rel is required for chromatin remodeling across the IL-2 gene promoter. J. Immunol. 170, 3724–3731 (2003)
    Article CAS Google Scholar
  12. Liu, Y. et al. A critical function for TGF-β signaling in the development of natural CD4+CD25+Foxp3+ regulatory T cells. Nature Immunol. 9, 632–640 (2008)
    Article ADS CAS Google Scholar
  13. Polansky, J. K. et al. DNA methylation controls Foxp3 gene expression. Eur. J. Immunol. 38, 1654–1663 (2008)
    Article CAS Google Scholar
  14. Maurange, C. & Paro, R. A cellular memory module conveys epigenetic inheritance of hedgehog expression during Drosophila wing imaginal disc development. Genes Dev. 16, 2672–2683 (2002)
    Article CAS Google Scholar
  15. Yao, Z. et al. Nonredundant roles for Stat5a/b in directly regulating Foxp3 . Blood 109, 4368–4375 (2007)
    Article CAS Google Scholar
  16. Ono, M. et al. Foxp3 controls regulatory T-cell function by interacting with AML1/Runx1. Nature 446, 685–689 (2007)
    Article ADS CAS Google Scholar
  17. Rudra, D. et al. Runx-CBFβ complexes control expression of the transcription factor Foxp3 in regulatory T cells. Nature Immunol. 10, 1170–1177 (2009)
    Article CAS Google Scholar
  18. Kitoh, A. et al. Indispensable role of the Runx1-Cbfβ transcription complex for _in vivo_-suppressive function of FoxP3+ regulatory T cells. Immunity 31, 609–620 (2009)
    Article CAS Google Scholar
  19. Bruno, L. et al. Runx proteins regulate Foxp3 expression. J. Exp. Med. 206, 2329–2337 (2009)
    Article ADS CAS Google Scholar
  20. Fontenot, J. D. et al. Regulatory T cell lineage specification by the forkhead transcription factor Foxp3. Immunity 22, 329–341 (2005)
    Article CAS Google Scholar
  21. Lee, E. C. et al. A highly efficient _Escherichia coli_-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73, 56–65 (2001)
    Article CAS Google Scholar
  22. Dubchak, I. & Ryaboy, D. V. VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes. Methods Mol. Biol. 338, 69–89 (2006)
    CAS PubMed Google Scholar
  23. Zheng, Y. et al. Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells. Nature 445, 936–940 (2007)
    Article ADS CAS Google Scholar
  24. Sather, B. D. et al. Altering the distribution of Foxp3+ regulatory T cells results in tissue-specific inflammatory disease. J. Exp. Med. 204, 1335–1347 (2007)
    Article CAS Google Scholar

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Acknowledgements

We thank T.-T. Chu and L. Karpik for expert technical assistance and mouse colony management, S. Roh for embryonic stem cell culture and screening, J. Rasmussen and A. Kas for bioinformatics support, A. Beg for providing c-Rel knockout mice, P. Treuting for histopathology analysis, J. Gerard for assistance in luciferase reporter assays, and C. Wilson, S. Tarakhovsky and L.-F. Lu for critical comments on the manuscript. This work was supported by grants from the National Institutes of Health (to A.Y.R.). Y.Z. and A.C. were supported by the CRI-Irvington Institute postdoctoral fellowship. S.Z.J. was supported by the CRI pre-doctoral training grant. A.Y.R. is an investigator with the Howard Hughes Medical Institute.

Author Contributions Y.Z. and S.J. performed and analysed the experiments, with assistance from A.C. in oligonucleotide pull-down and from X.P.P. in ChIP experiments. K.F. assisted with blastocysts injections. S.J., Y.Z. and A.Y.R. designed experiments and wrote the paper.

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Author notes

  1. Ye Zheng
    Present address: Present address: Salk Institute for Biological Studies, La Jolla, California 92037, USA.,
  2. Ye Zheng and Steven Josefowicz: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute and Department of Immunology, University of Washington, Seattle, Washington 98195, USA,
    Ye Zheng, Steven Josefowicz, Ashutosh Chaudhry, Katherine Forbush & Alexander Y. Rudensky
  2. Howard Hughes Medical Institute and Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA ,
    Ye Zheng, Steven Josefowicz, Ashutosh Chaudhry, Xiao P. Peng & Alexander Y. Rudensky

Authors

  1. Ye Zheng
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  2. Steven Josefowicz
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  3. Ashutosh Chaudhry
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  4. Xiao P. Peng
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  5. Katherine Forbush
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  6. Alexander Y. Rudensky
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Correspondence toAlexander Y. Rudensky.

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Zheng, Y., Josefowicz, S., Chaudhry, A. et al. Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate.Nature 463, 808–812 (2010). https://doi.org/10.1038/nature08750

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Editorial Summary

Foxp3 gene and T-cell fate

Regulatory T (Treg) cells act to suppress immune system activation, so tight control over their numbers and activity is an important part of immune homeostasis. Here it is shown that particular conserved non-coding sequence elements at the Foxp3 locus play a role in controlling the size and composition of the Treg-cell population.