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ABSTRACT The transcription factor Foxp3 participates dominantly in the specification and function of Foxp3+CD4+ regulatory T cells (Treg cells) but is neither strictly necessary nor

sufficient to determine the characteristic Treg cell signature. Here we used computational network inference and experimental testing to assess the contribution of other transcription

factors to this. Enforced expression of Helios or Xbp1 elicited distinct signatures, but Eos, IRF4, Satb1, Lef1 and GATA-1 elicited exactly the same outcome, acting in synergy with Foxp3 to

activate expression of most of the Treg cell signature, including key transcription factors, and enhancing occupancy by Foxp3 at its genomic targets. Conversely, the Treg cell signature was

robust after inactivation of any single cofactor. A redundant genetic switch thus 'locked in' the Treg cell phenotype, a model that would account for several aspects of Treg cell

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subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS RUNX FACTORS LAUNCH T CELL AND INNATE LYMPHOID PROGRAMS VIA DIRECT AND GENE NETWORK-BASED

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Samstein and A. Rudensky for the unpublished ChIP-seq data; S. Smale (University of California, Los Angeles) for mouse cDNA encoding Helios; M. Calderwood and the Center for Cancer Systems

Biology for expression cDNA; P. Rahl for advice on ChIP-Seq; J. Ericson, S. Davis, H. Paik and R. Cruse for genomic data analysis; H. Chen and Q. Cai for experimental support; and J.

LaVecchio and G. Buruzala for sorting. This work benefited from public data generated by the Immunological Genome Project consortium. Supported by the US National Institutes of Health

(AI051530 to C.B. and D.M.; AI072073 to C.B., D.M. and J.C.; training grant T32 DK7260 for support of M.S.F.; and 3R24AI072073-03S1 for support of A.E.), GlaxoSmithKline, the Damon Runyon

Cancer Research Foundation (S.H.), the American Diabetes Association (7-07-BETA-14 to W.F.) and the Canadian Institutes of Health Research (J.H.). AUTHOR INFORMATION Author notes * Jonathan

A Hill & Sokol Haxhinasto Present address: Present addresses: Tempero Pharmaceuticals, Cambridge, Massachusetts, USA (J.A.H.), and Boehringer Ingelheim Pharmaceuticals, Ridgefield,

Connecticut, USA (S.H.)., * Ayla Ergun and Ting Lu: These authors contributed equally to this work. AUTHORS AND AFFILIATIONS * Division of Immunology, Department of Microbiology and

Immunobiology, Harvard Medical School, Boston, Massachusetts, USA Wenxian Fu, Ayla Ergun, Jonathan A Hill, Sokol Haxhinasto, Marlys S Fassett, Diane Mathis & Christophe Benoist *

Department of Biomedical Engineering, Howard Hughes Medical Institute, and Center for BioDynamics, Boston University, Boston, Massachusetts, USA Ayla Ergun, Ting Lu & James J Collins *

Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA Ting Lu * Immune Disease Institute, Program in Cellular and Molecular Medicine,

Children's Hospital Boston, Boston, Massachusetts, USA Roi Gazit & Derrick Rossi * Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston,

Massachusetts, USA Stanley Adoro & Laurie Glimcher * Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France Susan Chan & Philippe Kastner Authors * Wenxian

Fu View author publications You can also search for this author inPubMed Google Scholar * Ayla Ergun View author publications You can also search for this author inPubMed Google Scholar *

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Scholar CONTRIBUTIONS W.F., A.E., T.L., M.S.F., J.A.H., S.A., J.J.C., D.M. and C.B. designed experiments; W.F., J.A.H., S.H., M.S.F. and R.G. did experiments; A.E. and T.L. did computation;

L.G., S.C., P.K. and D.R. provided mice and advice; and W.F., A.E., T.L., J.A.H., R.G., M.S.F., J.J.C., D.M. and C.B. analyzed data and wrote manuscript. CORRESPONDING AUTHORS Correspondence

to Diane Mathis or Christophe Benoist. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests. SUPPLEMENTARY INFORMATION SUPPLEMENTARY TEXT AND FIGURES

Supplementary Figures 1–8 and Note (PDF 2747 kb) SUPPLEMENTARY TABLE 1 Cell samples use for CLR prediction. (XLSX 16 kb) SUPPLEMENTARY TABLE 2 CLR predicted TFs and the number of genes they

influence in the Treg signature. (XLSX 13 kb) SUPPLEMENTARY TABLE 3 Expression of Treg signature genes in Tconv cells transduced with different retroviruses, as indicated. (XLSX 70 kb)

SUPPLEMENTARY TABLE 4 Expression of endogenous TFs in transduced cells (FoldChange from control). (XLSX 11 kb) SUPPLEMENTARY TABLE 5 Summary and primary data for ChIP-seq. (XLSX 9 kb)

SUPPLEMENTARY TABLE 6 Genome-wide FoxP3 binding in Tconv cells transduced with FoxP3, or FoxP3+GATA1. (XLSX 1187 kb) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE

THIS ARTICLE Fu, W., Ergun, A., Lu, T. _et al._ A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells. _Nat Immunol_ 13, 972–980

(2012). https://doi.org/10.1038/ni.2420 Download citation * Received: 13 February 2012 * Accepted: 13 August 2012 * Published: 09 September 2012 * Issue Date: October 2012 * DOI:

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