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

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. Overall design: Examination of 4 different histone modifications in LKS cells in vivo in H3.3BKO or H3.3A, H3.3B double KO (DKO) mice. Examination of H3.3 enrichment in wild type LKS cells in vitro or in vivo.