Aire expression is associated with transcription of Polycomb silenced genes in mTEC. (A) Metagene profiles of the average normalized enrichment of H3K4me3 against input for sets of genes distinguished by Aire dependence and tissue specificity. (B) Boxplots of the median enrichment of H3K4me3 at the TSS of these sets of genes. (C,D) The results of the corresponding analysis for H3K27me3 marks. In B and D, *** indicates a significance level of P < 0.001 using the Mann-Whitney U-test. (E) The association of genes up-regulated by Aire expression (>2×, FDR < 0.05, Aire-positive vs. Aire-knockout mTEC) with genes whose TSS (1-kb centered windows) showed an average (n = 2) twofold or greater enrichment for H3K27me3 or H3K4me3 marks over input. Stated P-values were calculated using Fisher’s exact test. (F) Enrichment of H3K4me3 and H3K27me3, respectively, for the TSS of all protein-coding genes. Those induced by Aire expression are highlighted in red. The dashed box highlights a subset of genes induced by Aire expression whose TSS show enrichments for both modifications. (G) Genes induced by Aire expression are generally weakly transcribed in Aire-KO mTEC and have relatively low H3K4me3 enrichment scores and relatively high H3K27me3 enrichment scores. The heatmap shows all genes ordered by their ratio of expression in mature Aire-positive and knockout TEC. (H) The chromatin state and expression of APS-1 autoantigen ortholog Sox10 and Polr2f encoding a RNA Pol II subunit in mature mTEC.
