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Genome-wide maps of histone modifications in hematopoietic stem cells in control or H3.3 null LKS cells.

ABSTRACT: In order to understand the epigenetic events following the deletion of histone variant H3.3 in mouse hematopoieitc stem cells both in vitro or in vivo (Rosa26creERT2+ H3.3Af/f, H3.3B -/- mice), we sorted cKit+Sca1+Lin- HSPCs and utilized an MNase based native ChIP protocol to characterize the four types of histone modifications H3K27me3, H3K9me3, H3K27ac and H3K4me3 changes. Matching with the biased granulocyte-macrophage progenitor differentiation potential of H3.3 null HSPCs, we found that there is significant global gain of H3K27me3 marks when H3.3 is deleted. Conversely, there is a predominant loss of H3K9me3 marks globably in H3.3 null HSPCs. We hypothesize that the gain of H3K27me3 marks is what udnerlines the dimished stemness and lineage differentiation capacities toward red blood cell lineages, the mimicing of GMPs for H3.3 null HSPCs. On the other hand, loss of H3K9me3 at ERV regions derepssed ERVs and induces interferon responses. The H3K9me3 reduced/ERV regions may serve as enhancer regions for transcription factors to bind and might confer the H3.3 null HSPCs adaptive advantage for enhanced survival.

ORGANISM(S): Mus musculus

PROVIDER: GSE148750 | GEO | 2021/04/30

REPOSITORIES: GEO

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Project description:Epigenetic environment of histone H3.3 on promoters revealed by integration of imaging and genome-scale chromatin and methyl-DNA immunoprecipitation information. Chromatin regions with different transcriptional outputs are distinguished by the deposition of histone variants. Histone H3.3 is incorporated into chromatin in a replication-independent manner; yet the relationship between H3.3 deposition, chromatin environment is incompletely understood. We have integrated imaging and genome-scale chromatin and methyl-DNA immunoprecipitation approaches to investigate the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation and transcription. Results: Imaging shows that H3.3, in contrast to replicative H3.1 or H2B, is enriched in chromatin marked by histone modifications of active genes. A genome-wide survey identifies 1,649 H3.3-enriched promoters, only a subset of which is co-enriched in H3K4me3, H3K9me3 and/or H3K27me3, with a preference for H3K4me3, corroborating imaging data. H3.3-enriched promoters are depleted of H3.3 at the TSS in a transcription-independent manner. H3.3 is found predominantly on CpG-rich unmethylated promoters, creating a condition favourable for transcription. In undifferentiated mesenchymal stem cells, H3.3 target genes are linked to signaling and mesodermal differentiation, suggesting that H3.3 may be a mark of lineage priming. Conclusions: A minor fraction of H3.3 is targeted to promoters, which are predominantly CpG-rich, DNA unmethylated and devoid of detectable trimethylated H3K4, K9 and K27. Among H3.3 target promoters co-marked by methylated H3, H4K4me3 is preferred, with or without H3K27me3, arguing that in mesenchymal stem cells H3.3 marks transcriptionally active or potentially active promoters. Key words: Imaging, ChIP-chip, MeDIP-chip, histone H3.3, mesenchymal stem cells ChIP-chip and MeDIP-chip experiments: Performed with two independent biological replicates. Gene expression profiling experiments: Total RNA obtained from H3.3-EGFP transfected or empty-EGFP transfected mesenchymal stem cells compared to untransfected mesenchymal stem cells. Raw expression data linked below as supplementary file (GSE17053_Illumina_non-normalized_data.txt).

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Genome-wide maps of histone modifications in hematopoietic stem cells in control or H3.3 null LKS cells.

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