Abstract
BackgroundThe hierarchical organization of eukaryotic chromatin plays a central role in gene regulation, by controlling the extent to which the transcription machinery can access DNA. The histone variants H3.3 and H2A.Z have recently been identified as key regulatory players in this process, but the underlying molecular mechanisms by which they permit or restrict gene expression remain unclear. Here, we investigated the regulatory function of H3.3 and H2A.Z on chromatin dynamics and Polycomb-mediated gene silencing.ResultsOur ChIP-seq analysis reveals that in mouse embryonic stem (mES) cells, H3K27me3 enrichment correlates strongly with H2A.Z. We further demonstrate that H2A.Z promotes PRC2 activity on H3K27 methylation through facilitating chromatin compaction both in vitro and in mES cells. In contrast, PRC2 activity is counteracted by H3.3 through impairing chromatin compaction. However, a subset of H3.3 may positively regulate PRC2-dependent H3K27 methylation via coordinating depositions of H2A.Z to developmental and signaling genes in mES cells. Using all-trans retinoic acid (tRA)-induced gene as a model, we show that the dynamic deposition of H2A.Z and H3.3 coordinately regulates the PRC2-dependent H3K27 methylation by modulating local chromatin structure at the promoter region during the process of turning genes off.ConclusionsOur study provides key insights into the mechanism of how histone variants H3.3 and H2A.Z function coordinately to finely tune the PRC2 enzymatic activity during gene silencing, through promoting or impairing chromosome compaction respectively.
Highlights
The hierarchical organization of eukaryotic chromatin plays a central role in gene regulation, by controlling the extent to which the transcription machinery can access DNA
In contrast to the case of H2A.Z, only weak co-localization as well as low correlations was observed for H3.3 with H2A.Z or H3K27me3 at the regions enriched with H3K27me3 in mouse embryonic stem (mES) cells (Fig. 1a, b, Additional file 1: Figure S1B to S1D)
The zero point of x-axis corresponds with the center of each H3K27me3 peak and expands from 5 kb upstream to 5 kb downstream to form H3K27me3 peak regions. b Scatterplot for the average reads density of H3K27me3, H2A.Z, and H3.3 at the H3K27me3-enriched regions. c The schematic view of mononucleosomes immuno-precipitation (Mono-IP), stable overexpressed histone H2A, or H2A.Z mouse R1 ES cell line was generated and applied here. d Histone modifications associated with H2A- and H2A.Z-containing mononucleosomes
Summary
The hierarchical organization of eukaryotic chromatin plays a central role in gene regulation, by controlling the extent to which the transcription machinery can access DNA. Chromatin organization from its basic nucleosomal structure to the more complex higher-order chromatin structures restricts the access of cellular factors/machinery to DNA. Histone variants H2A.Z and H3.3, both of which are essential for multicellular organisms [9, 10], have been demonstrated to play crucial and specific roles in regulating chromatin structure and functions during development and in diseases [11, 12]. Genome-wide studies in a variety of organisms show that H2A.Z is enriched at the promoter of inducible genes under repressed or basal expression conditions, but is subsequently removed upon transcriptional activation [18, 19]. H3.3 is incorporated in mES cells at the heterochromatic regions of the genome such as telomere, pericentric heterochromatin, and retroviral elements [26, 27]
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