Aire employs a histone-binding module to mediate immunological tolerance, linking chromatin regulation with organ-specific autoimmunity - PubMed (original) (raw)

. 2008 Oct 14;105(41):15878-83.

doi: 10.1073/pnas.0808470105. Epub 2008 Oct 7.

Alex J Kuo, Sang Youn Park, Peggie Cheung, Jakub Abramson, Dennis Bua, Dylan Carney, Steven E Shoelson, Or Gozani, Robert E Kingston, Christophe Benoist, Diane Mathis

Affiliations

Aire employs a histone-binding module to mediate immunological tolerance, linking chromatin regulation with organ-specific autoimmunity

Andrew S Koh et al. Proc Natl Acad Sci U S A. 2008.

Abstract

Aire induces ectopic expression of peripheral tissue antigens (PTAs) in thymic medullary epithelial cells, which promotes immunological tolerance. Beginning with a broad screen of histone peptides, we demonstrate that the mechanism by which this single factor controls the transcription of thousands of genes involves recognition of the amino-terminal tail of histone H3, but not of other histones, by one of Aire's plant homeodomain (PHD) fingers. Certain posttranslational modifications of H3 tails, notably dimethylation or trimethylation at H3K4, abrogated binding by Aire, whereas others were tolerated. Similar PHD finger-H3 tail-binding properties were recently reported for BRAF-histone deacetylase complex 80 and DNA methyltransferase 3L; sequence alignment, molecular modeling, and biochemical analyses showed these factors and Aire to have structure-function relationships in common. In addition, certain PHD1 mutations underlying the polyendocrine disorder autoimmune polyendocrinopathy-candidiases-ectodermaldystrophy compromised Aire recognition of H3. In vitro binding assays demonstrated direct physical interaction between Aire and nucleosomes, which was in part buttressed by its affinity to DNA. In vivo Aire interactions with chromosomal regions depleted of H3K4me3 were dependent on its H3 tail-binding activity, and this binding was necessary but not sufficient for the up-regulation of genes encoding PTAs. Thus, Aire's activity as a histone-binding module mediates the thymic display of PTAs that promotes self-tolerance and prevents organ-specific autoimmunity.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Fig. 1.

Aire recognizes the unmodified N terminus of H3 tail via PHD1. (A) Histone peptide microarray containing the indicated modifications was probed with GST-mAire294–350 or GST-mAire425–481. Red spots indicate GST-specific signals. H indicates histone; me, methylation; ac, acetylation; ph, phosphorylation; s, symmetric; a, asymmetric. (B) Anti-GST Western blots of histone peptide pulldowns with indicated biotinylated peptides and GST-mAirePHD1 or PHD2 fusion proteins. (C) Peptide pulldowns as in B except with full-length WT, D299A, or ΔPHD2 Aire-flag. (D) Comparisons of PHD fingers from BHC80, hAIRE, mAire, and DNMT3L. Blue indicates Zn2+-chelating residues. Red indicates H3K4me0-binding residues. Red underscore indicates antiparallel β-strand-engaging H3 peptide. Pink indicates residues that insert between H3R2me0 and H3K4me0 and interact with H3 side chains. Yellow indicates hydrophobic pocket specific to H3A1. Turquoise box indicates hydrogen bond cage recognizing N terminus of H3. Black indicates predicted H3R2me0-interacting residue. Green indicates APECED mutations: V301M (identified in patient with autoimmune Addison's disease, ref. 46), C311Y, and P326L/Q. (E) Peptide pulldowns as in B except with critical binding and APECED mutations.

Fig. 2.

Fig. 2.

Dissociation constants of mAire's recognition of the N terminus of the H3 tail as measured by ITC.

Fig. 3.

Fig. 3.

Recognition of H3 tail contributes to Aire's in vivo interaction with chromatin. (A) Aire ChIP. The 4D6 (Upper) or 293T (Lower) cells transfected with tagged WT or D299A were Flag-ChIPed, followed by Western blotting with the indicated antibodies (α-). Percentages of total ChIPed or input were loaded as indicated. Relative band intensities are in bold below respective bands. (B) Histones associated with Aire in vivo are H3K4me3-depleted. The 293T ChIP is as in A.

Fig. 4.

Fig. 4.

Recognition of H3 tail is crucial for Aire's ectopic expression of PTA in vivo. (A) Quantitative RT-PCR of total RNA from 4D6 cells transfected with WT or mutant Aire representative of four independent experiments. Enrichment of endogenous PTA mRNA represents normalized levels to internal HPRT and mock transfections. (B) Expression levels from transfection. Western blots of 4D6 whole-cell lysates with indicated antibodies.

References

    1. Hogquist KA, Baldwin TA, Jameson SC. Central tolerance: Learning self-control in the thymus. Nat Rev Immunol. 2005;5:772–782. - PubMed
    1. Kyewski B, Klein L. A central role for central tolerance. Annu Rev Immunol. 2006;24:571–606. - PubMed
    1. Anderson MS, et al. Projection of an immunological self shadow within the thymus by the Aire protein. Science. 2002;298:1395–1401. - PubMed
    1. Liston A, et al. Aire regulates negative selection of organ-specific T cells. Nat Immunol. 2003;4:350–354. - PubMed
    1. Anderson MS, et al. The cellular mechanism of Aire control of T cell tolerance. Immunity. 2005;23:227–239. - PubMed

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