Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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


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.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: Conserved non-coding sequences and chromatin modifications at the Foxp3 locus.
Figure 2: CNS3 controls de novo Foxp3 expression.
Figure 3: CNS1 controls peripheral, but not thymic, induction of Foxp3 expression.
Figure 4: CNS2 controls the heritable maintenance of Foxp3 expression.


  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 

Download references


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.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Alexander Y. Rudensky.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figure 1-19 with Legends and Supplementary Tables 1-2. (PDF 1146 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing