To gain insights into how pancreatic beta-cells are programmed in vivo, we profiled key histone methylations (H3K4/K27me3) in embryonic stem cells, multipotent progenitors of the nascent embryonic pancreas, purified beta-cells, and 10 other adult tissues (all under normal, untreated conditions). For these cells we also purified RNA to analyze tissue specific genome wide transcription levels in relation to histone modifications. This study refers to the epigenomics component of such work. Corresponding RNA microarrays can be found in Array Express under accession E-TABM-906.

Gain insights into how beta cells are programmed.

Key histone methylations were profiled in embryonic stem cells (CGR8), multipotent progenitors of the embryonic pancreas, purified beta cells, and 10 differentiated tissues (10- to 16-wk-old C57Bl/6J male mice). Pdx1-expressing progenitors were obtained by dissecting E10.5 pancreatic buds of Pdx1-eGFP mice followed by FACS. Immunoprecipitations were performed with anti-H3K4me3 (Upstate, 05-745), anti-H3K27me3 (Upstate, 07-449), mouse monoclonal anti-REST (12C11 (Dr. David J. Anderson, California Institute of Technology, Pasadena), or anti-mouse IgG (Abcam, ab6709). Genes were classified according to the presence or absence of H3K27me3 and H3K4me3 enrichment at +/- 2 kb from the transcriptional start site of 16,523 RefSeq genes using Affymetrix GeneChip Mouse Promoter 1.0R Arrays.

Two major classes of H3K27me3 targets were found: (1) CpG-island genes that are already enriched in H3K27me3 in ES cells, and either maintain H3K27me3 or undergo tissue-selective loss of H3K27me3 during differentiation, and (2) genes in which H3K27me3 is not present in ES cells but instead arises de novo. Bivalent H3K4me3 and H3K27me3 enrichment was found in differentiated tissues or purified beta-cells in numerous genes and these genes were generally inactive. REST binds in ES cells to genes that form the beta-cell selective lack of Polycomb group (PcG) repression program. The expression of REST is extinguished in Neurog3+ pancreatic endocrine progenitors and acquires the H3K27me3 repressive mark after the pancreatic precursor stage during beta-cell differentiation. Beta-cell-specific gene activity is to a large extent determined by the selective loss of H3K27me3 in genes that show a bivalent chromatin state in ES cells. Selective absence of PcG repression in beta cells included many known beta-cell enriched transcriptional regulators and also included many previously unrecognized putative regulators of beta cells, such as Tox3 and Lhx1.

Beta cells show an active chromatin signature that is most similar to ectoderm-derived neural tissues. As part of the same investigation, beta cells and neural tissues were found to share a gene activity profile. In contrast, the beta-cell signature of trimethylated H3K27, a mark of Polycomb-mediated repression, clusters with pancreatic progenitors, acinar cells and liver, consistent with the epigenetic transmission of this mark from endoderm progenitors to their differentiated cellular progeny.

• comparison of endocrine and/or exocrine cell populations: 3446, 3687, 3834, 4114, 4135, 4395,
• islet epigenomics: 3918, 4075, 4078, 4114, 4175, 4235, 4395, 4514,