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Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing transcription of the gene encoding interferon-γ

Nature Immunology volume 8, pages 732–742 (2007)Cite this article

A Corrigendum to this article was published on 01 January 2008

A Corrigendum to this article was published on 01 December 2007

A Corrigendum to this article was published on 01 August 2007

This article has been updated

Abstract

Unlike the well defined T helper type 2 cytokine locus, little is known about the regulatory elements that govern the expression of Ifng, which encodes the 'signature' T helper type 1 cytokine interferon-γ. Here our evolutionary analysis showed that the mouse Ifng locus diverged from the ancestral locus as a result of structural rearrangements producing deletion of the neighboring gene encoding interleukin 26 and disrupting synteny 57 kilobases upstream of Ifng. Proximal to that disruption, we identified by high-resolution mapping many regions with CD4+ T cell subset–specific epigenetic modifications. A subset of those regions represented enhancers, whereas others blocked the activity of upstream enhancers or insulated Ifng from neighboring chromatin. Our findings suggest that proper expression of Ifng is maintained through the collective action of multiple distal regulatory elements present in a region of about 100 kilobases flanking Ifng.

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Figure 1: Evolutionary conservation in the Ifng locus.
Figure 2: DNase-hypersensitivity profiling shows lineage-specific changes in DNase hypersensitivity.
Figure 3: TH1 cells are 'marked' by K4(me2), whereas naive and TH2 cells are characterized by enrichment for K27(me3).
Figure 4: CD4+ T cell subset–specific CpG methylation at the Ifng locus.
Figure 5: Epigenetic profiles of naive, TH1 and TH2 CD4+ T cells.
Figure 6: IfngCNS–6 and IfngCNS+29 enhance IFN-γ production in the absence of T-bet; IfngCNS–22 and IfngCNS–34 are T-bet-dependent enhancers.
Figure 7: Ifng CNSs enhance Ifng expression in NK cells and primary T cells.
Figure 8: Boundary function of CNSs.

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Change history

  • 05 July 2007

    In the version of this article initially published, the surname of the penultimate author is misspelled. The correct spelling is Stamatoyannopoulos. The error has been corrected in the HTML and PDF versions of the article.

  • 16 November 2007

    In the version of this article initially published, labels in Figures 2 and 4 are incorrect (as is the relevant text for Figure 4), and a reagent is incorrectly identified in Methods. In Figure 2, the label “IfngCNS+54” should be “IfngCNS+55.” For Figure 4, the primers used to analyze the intronic region of Ifng for CpG methylation after bisulfite treatment amplify intron 1; thus, the label above the sixth column in Figure 4a should be “Ifng intron 1” and the accompanying text on page 736, column 1, should read “intron 1” on lines 3 and 13. In the Methods section, page 740 column 2, the end of line 23 should read “rabbit immunoglobulin G.” The errors have been corrected in the PDF version of the article.

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Acknowledgements

We thank C. Surh (Scripps Research Institute) and M. Bevan (University of Washington) for Thy-1.1+ SMARTA TCR-transgenic mice; T. Krumm (University of Washington) and M. Krangel (Duke University) for the Eδ-Pδ-βNeo-scs′ and Pδ-BNeo-scs′ constructs; M. Kaja for LCMV Armstrong; K. Arispe and M. Weaver for technical assistance; S. Taylor for an earlier computational analysis of the Ifng locus; and E. Eichler and M. Orr for comments. Supported by the National Institutes of Health (AI071272 and HD18184; and CA009537 to J.R.S.), the March of Dimes and the Cancer Research Institute (J.R.S.).

Author information

Author notes

  1. Michael O Dorschner and Masayuki Sekimata: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Immunology, University of Washington, Seattle, 98195, Washington, USA

    Jamie R Schoenborn, Masayuki Sekimata, Deanna M Santer, Maria Shnyreva & Christopher B Wilson

  2. Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, 98195, Washington, USA

    Jamie R Schoenborn

  3. Department of Medicine, University of Washington, Seattle, 98195, Washington, USA

    Michael O Dorschner & John A Stamatoyannopoulos

  4. Department of Genome Sciences, University of Washington, Seattle, 98195, Washington, USA

    Michael O Dorschner & John A Stamatoyannopoulos

  5. PO Box 270514, Fort Collins, 80527, Colorado, USA

    David R Fitzpatrick

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Contributions

J.R.S. designed and did research, analyzed data and wrote the paper; M.O.D. designed and did research and analyzed data; M. Sekimata did research and analyzed data; D.M.S. did research and analyzed data; M. Shnyreva did the chromatin immunoprecipitation of D10 and AE7 cells; D.R.F. contributed intellectually and helped write the paper; J.A.S. designed research; C.B.W. designed research, analyzed data and wrote the paper; and all authors reviewed the paper before submission.

Corresponding author

Correspondence to Christopher B Wilson.

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Competing interests

D.R.F. is a former employee and shareholder of Amgen.

Supplementary information

Supplementary Fig. 1

The rodent Ifng locus contains a complex set of structural rearrangements and segmental duplications beginning 57 kb upstream of Ifng that has disrupted Il26. (PDF 180 kb)

Supplementary Fig. 2

Generation and production of IFN-γ by in vitro TH1 and TH2 cultures or in vivo CD4+ effectors. (PDF 110 kb)

Supplementary Fig. 3

ChIP for total histone H3 in the Ifng locus in naive, TH1 or TH2 CD4+ T cells. (PDF 84 kb)

Supplementary Fig. 4

ChIP for acetylated histone H3 in the Ifng locus in long-term TH1 (AE7) and TH2 (D10) cell lines. (PDF 60 kb)

Supplementary Table 1

Location of DNase HS sites in primary CD4 naive, TH1 and TH2 cells. (PDF 30 kb)

Supplementary Table 2

Chromatin immunoprecipitation primers. (PDF 11 kb)

Supplementary Table 3

Primers used in DNase HS analysis based off of mm8 C57BL/6 sequence (Ifng start at 117844040). (PDF 40 kb)

Supplementary Table 4

BIS-PCR primers for CpG methylation analysis. (PDF 50 kb)

Supplementary Methods (PDF 11 kb)

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Schoenborn, J., Dorschner, M., Sekimata, M. et al. Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing transcription of the gene encoding interferon-γ. Nat Immunol 8, 732–742 (2007). https://doi.org/10.1038/ni1474

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