Abstract
BackgroundBivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks. Existence of such bivalent marks on the same nucleosome has only recently been suggested. Previous genome-wide efforts to characterize bivalent chromatin have focused primarily on individual marks to define overlapping zones of bivalency rather than mapping positions of truly bivalent mononucleosomes.ResultsHere, we developed an efficacious sequential ChIP technique for examining global positioning of individual bivalent nucleosomes. Using next generation sequencing approaches we show that although individual H3K4me3 and H3K27me3 marks overlap in broad zones, bivalent nucleosomes are focally enriched in the vicinity of the transcription start site (TSS). These seem to occupy the H2A.Z nucleosome positions previously described as salt-labile nucleosomes, and are correlated with low gene expression. Although the enrichment profiles of bivalent nucleosomes show a clear dependency on CpG island content, they demonstrate a stark anti-correlation with methylation status.ConclusionsWe show that regional overlap of H3K4me3 and H3K27me3 chromatin tend to be upstream to the TSS, while bivalent nucleosomes with both marks are mainly promoter proximal near the TSS of CpG island-containing genes with poised/low expression. We discuss the implications of the focal enrichment of bivalent nucleosomes around the TSS on the poised chromatin state of promoters in stem cells.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-016-0221-6) contains supplementary material, which is available to authorized users.
Highlights
Bivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks
Most maps of histone modifications are created by performing chromatin immunoprecipitation (ChIP) on formaldehyde-crosslinked chromatin fractionated either by sonication or limited digest with micrococcal nuclease (MNase)
When we examined the transcriptionally active MLH1 promoter in SW480, we observed enrichment only in sequential ChIP directed against 1°H3K4me3 → 2°H3, used as positive controls, but no enrichment in samples subjected to 1° anti-H3K4me3 pull-down followed by 2° anti-H3K27me3 pull-down (Fig. 1e-f)
Summary
Bivalent chromatin refers to overlapping regions containing activating histone H3 Lys trimethylation (H3K4me3) and inactivating H3K27me marks. Local epigenetic control lies in positioning of nucleosomes around transcription start sites (TSS) and control regions, along with post-translational modifications of histone tails and/or the presence of non-canonical histone variants such as H2A.Z and H3.3 [1, 2]. These dynamics exert a combinatorial effect on gene expression states alone or in sync with differential states of DNA methylation at CpGs throughout the genome [3,4,5,6]. It is important to understand the precise constitution of the chromatin states with respect to normal and abnormal gene expression, especially bivalent chromatin
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