Genome-wide analysis of chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells. Mus musculus

Recent studies have shown that histone H2A and H3 have several variants which are differently distributed in the various genomic regions, suggesting that they are involved in the regulation of a variety of genome functions. However, in each of these studies, only a single or a few variants have been analyzed. In the present study, we examined the genome wide distribution of most of H2A and H3 variants (H2A, H2AX, H2AZ, macroH2A, H3.1, H3.2 and H3.3) in mouse ES cells by ChIPseq. The enrichment of H2A.Z and H3.3 in the promoters and bodies of genes were well correlated with the gene expression levels and that of macroH2A in gene bodies showed a reverse correlation. Around the transcription start site (TSS), the distribution of histone variants was prominently different between the genes whose promoters are of high and low CpG densities (HCP and LCP promoters, respectively). In the genes with HCP promoter but not LCP one, all of H2A and H3 variants except for H2A.Z were depleted at TSS regardless of their expression levels. In the vicinity of TSS, H2A.Z and H3.3 were highly enriched in the genes with HCP promoter but not those with LCP promoter. In the intergenic regions, regulatory elements, i.e. enhancers, CpG islands, and insulators, H2A.Z and H3.3 were enriched, whereas in repeat elements, H2A and macroH2A, and H3.1 were abundant. An analysis for the combination of H2A and H3 variants composing nucleosomes revealed that the occurrence rate of the combination of H2A.Z and H3.3 was high all through the genome when compared to other combinations, suggesting that H2A.Z and H3.3 are preferentially associated with each other to compose the nucleosomes independently of genome regions. Finally, we found that chromatin is unstable only in the regions where it is enriched in both of H2A.Z and H3.3. Therefore, the composition of histone variants seems to be important for the determination of chromatin structure which is associated with various genome functions.