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Chromatin remodeling and dynamics of hematopoietic stem cells and progenitors

ABSTRACT: Hematopoietic stem cells (HSCs) have the capability to self-renew and differentiate into all blood cell lineages. How chromatin state regulates self-renewal and differentiation of HSC is not fully understood. Here, we provided the first global landscape of chromatin state in long term (LT)-HSCs, short term (ST)-HSCs and multipotent progenitor (MPP) by ATAC-seq analysis. We discovered that the promoter regions of genes that control cell cycle, and several important miRNAs were maintained as open chromatin state in HSCs. In addition, we found that promoter-TSS regions of many genes were occupied by nucleosomes in LT/ST-HSC and they become open chromatin regions in MPP. Furthermore, we uncovered 166 known transcription factors (TFs) including C/EBPs, GABPA, and FLI1can access to the promoter open chromatin in HSCs, and quarter of them displayed cell type-specific manner. Among them, we identified DNA cis-element of Krüppel-like factor family (KLF9, KLF10 and KLF14) were specifically enriched in LT-HSC. Meanwhile, we found that 8299 enhancers are established concomitantly with the formation of open chromatin sites, and they can be accessed by 153 TFs including GABPA, CTCF and RNUX1/RUNX2. Near hundred TF-binding motif are enriched in both promoter and enhancers, indicating they may direct the interaction between promoters and enhancers. Finally, we found 21.7% poised enhancers were preset in LT/ST-HSCs, and became active enhancers in MPP. Together, our finding provides new insightinto how chromatin state and transcriptionalregulatory networkare remodeledin promoter and enhancer regions during the differentiation of LT/ST-HSC to MPP.

ORGANISM(S): Mus musculus

PROVIDER: GSE84959 | GEO | 2017/06/05

SECONDARY ACCESSION(S): PRJNA335747

REPOSITORIES: GEO

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