Aire is a transcriptional regulator that induces promiscuous expression of thousands of genes encoding tissue-restricted antigens (TRAs) in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs that regulate its own expression have remained elusive. Here we comprehensively analyzed both cis-acting and trans-acting regulatory mechanisms and found that the Aire locus was insulated by the global chromatin organizer CTCF and was hypermethylated in cells and tissues that did not express Aire. In mTECs, however, Aire expression was facilitated by concurrent eviction of CTCF, specific demethylation of exon 2 and the proximal promoter, and the coordinated action of several transcription activators, including Irf4, Irf8, Tbx21, Tcf7 and Ctcfl, which acted on mTEC-specific accessible regions in the Aire locus.

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We thank M. Anderson (University of California at San Francisco) for Aire-Igrp-GFP mice; D. Graf (University of Zurich) for B6.Foxn1-Cre mice (obtained with the consent of N. Manley (University of Georgia)); H. Clevers (Hubrecht Institute) for Tcf7−/− mice; and Y. Peleg, G. Yona and V. Krupalnik for experimental expertise and help. Supported by the Israel Science Foundation (1825/10 and 1376/13), the Sy Syms Foundation, the Dr. Celia Zwillenberg-Fridman and Dr. Lutz Fridman Career Development Chair (J.A.), the Weizmann-German Cancer Research Center PhD fellowship program (Y.H., M.D., J.A., M.F.), the German Cancer Research Center–Israeli Ministry of Science and Technology foundation for German-Israeli co-operation (2431 to J.A. and M.F.), the Agence Nationale de Recherche (2011-CHEX-001-R12004KK to M.Gi.) and the European Federation of Immunological Societies fellowship program (M.R.B.).

Author information


  1. Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.

    • Yonatan Herzig
    • , Shir Nevo
    • , Chamutal Bornstein
    • , Miriam R Brezis
    • , Sharon Ben-Hur
    • , Aya Shkedy
    • , Michal Eisenberg-Bord
    • , Ben Levi
    • , Yael Goldfarb
    • , Eyal David
    • , Ido Amit
    •  & Jakub Abramson
  2. Research Group Immune Tolerance, Tumor Immunology Program, German Cancer Research Center, Heidelberg, Germany.

    • Michael Delacher
    •  & Markus Feuerer
  3. Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

    • Leehee Weinberger
    • , Sergey Viukov
    •  & Jacob H Hanna
  4. Bioinformatics Unit, Biological Services Department, Weizmann Institute of Science, Rehovot, Israel.

    • Shifra Ben-Dor
  5. Department of Infection Immunity and Inflammation, Cochin Institute, Paris, France.

    • Matthieu Giraud
  6. Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.

    • Achim Breiling
    •  & Frank Lyko


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Y.H. and J.A. designed the study and wrote the manuscript; Y.H. performed most of the experimental work; S.N. performed several experiments, including ChIP, protein immunoprecipitation and Aire intracellular staining; C.B. performed the 'indexing-first' ChIP and ATAC-Seq experiments; M.R.B set up and conducted luciferase-based assays and analyzed the Tbx21-mutant mice; L.W. and S.V. constructed the Tet1fl/flTet2fl/flTet3fl/fl mice; M.D. assisted in performing the DNA bisulfite experiments; and S.B.-H., A.S., M.E.-B., Y.G., B.L., E.D., S.B.-D., M.G., J.H.H., A.B., F.L., I.A., M.F. and J.A. helped in performing, analyzing and/or designing some of the experiments.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jakub Abramson.

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