Genome-wide analysis of histone modifications in human pancreatic islets

Abstract

The global diabetes epidemic poses a major challenge. Epigenetic events contribute to the etiology of diabetes; however, the lack of epigenomic analysis has limited the elucidation of the mechanistic basis for this link. To determine the epigenetic architecture of human pancreatic islets we mapped the genome-wide locations of four histone marks: three associated with gene activation-H3K4me1, H3K4me2, and H3K4me3-and one associated with gene repression, H3K27me3. Interestingly, the promoters of the highly transcribed insulin and glucagon genes are occupied only sparsely by H3K4me2 and H3K4me3. Globally, we identified important relationships between promoter structure, histone modification, and gene expression. We demonstrated co-occurrences of histone modifications including bivalent marks in mature islets. Furthermore, we found a set of promoters that is differentially modified between islets and other cell types. We also use our histone marks to determine which of the known diabetes-associated single-nucleotide polymorphisms are likely to be part of regulatory elements. Our global map of histone marks will serve as an important resource for understanding the epigenetic basis of type 2 diabetes.

Figure 1.

Input-normalized modification levels of H3K4me1 (A), H3K4me2 (B), H3K4me3 (C), and H3K27me3 (D) depend on expression level and promoter type. Transcriptional start sites with a nearby CpG island (CpG+, yellow) show a relatively constant distribution of the H3K4me1 and H3K4me2 modifications levels that does not strongly correlate with gene expression. H3K4me3 levels are correlated with gene expression, even though they exhibit large variability. On the other hand, CpG− promoters (green) are usually unmodified except at high expression levels, where they begin to show higher levels of modifications. Thus, for the most part, the correlation of histone modifications and gene expression is due to a gradual increase in the proportion of CpG+ promoters at higher expression levels. The distribution of H3K27me3 is different, in accordance with its association with repression. At low expression levels, both CpG− and CpG+ promoters are occupied, and the overall levels of H3K27me3 modification decrease with increasing expression.

Figure 2.

Co-occurrence of input-normalized histone modification near the promoters (0–2000 bp) in human islets: (A) H3K4me2 vs. H3K4me1, (B) H3K4me3 vs. H3K4me2, (C) H3K4me3 vs. H3K4me1, and (D) H3K27me3 vs. H3K4me3. (A–C) The H3K4me1,2,3 series tends to either be completely absent (values near 1), or to co-occur (values near the diagonal). (D) H3K27me3 and H4K4me3 tend not to co-occur, with a few exceptions (bivalent genes).

Figure 3.

Marks of active and repressed genes in islets. (A) Human islet chromatin enriched for H3K4me1, H3K4me2, H3K4me3, H3K27me3, and control input DNA from four samples was processed and sequenced. Reads were pooled and aligned to the NCBI Genome Build 36.1-hg18, to determine regions that were enriched for binding by modified histones. Note the strong double peak surrounding the transcriptional start site (left end) of ATF4, and the weaker peaks for H3K4me1 and H3K4me2. In B, the HOXB cluster contains significantly enriched regions for H3K27me3 as well as H3K4me3 at several transcription start sites.

Figure 4.

Comparison of H3K4me3 at gene promoters in human islets and CD4+ T-cells. The square root of the summary input-normalized levels of H3K4me3 for CpG island-containing (yellow) and CpG island-less (green) genes are plotted. The CpG island-less genes in the magenta (395 genes) and blue (93 genes) boxes are modified only in one tissue or the other, indicating that this class of genes exhibits tissue-specific promoter modification.