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Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos.

ABSTRACT: Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos.

PROVIDER: PRJNA677885 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13040500_1.fastq.gz	Fastqsanger.gz
	SRR13040500_2.fastq.gz	Fastqsanger.gz
	SRR13040501_1.fastq.gz	Fastqsanger.gz
	SRR13040501_2.fastq.gz	Fastqsanger.gz
	SRR13040502_1.fastq.gz	Fastqsanger.gz

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Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos [Hi-C]

Project description:Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos [Hi-C]

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Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos [ChIP-seq]

Project description:Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos [ChIP-seq]

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Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos.

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-12-12 | GSE161328 | GEO

Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos.

Project description:The gene activity underlying cell differentiation is regulated by a diverse set of transcription factors (TFs), histone modifications, chromatin structures and more. Although definitive hematopoietic stem cells (HSCs) are known to emerge via endothelial-to-hematopoietic transition (EHT), how the multi-layered epigenome is sequentially unfolded in a small portion of endothelial cells (ECs) transitioning into the hematopoietic fate remains elusive. With optimized low-input itChIP-seq and Hi-C assays, we performed multi-omics dissection of the HSC ontogeny trajectory across early arterial ECs (eAECs), hemogenic endothelial cells (HECs), pre-HSCs and long-term HSCs (LT-HSCs) in mouse embryos. Interestingly, HSC regulatory regions are already pre-configurated with active histone modifications as early as eAECs, preceding chromatin looping dynamics within topologically associating domains. Chromatin looping structures between enhancers and promoters only become gradually strengthened over time. Notably, RUNX1, a master TF for hematopoiesis, enriched at half of these loops is observed early from eAECs through pre-HSCs but its enrichment further increases in HSCs. RUNX1 and co-TFs together constitute a central, progressively intensified enhancer-promoter interactions. Thus, our study provides a framework to decipher how temporal epigenomic configurations fulfill cell lineage specification during development.

| S-EPMC8764075 | biostudies-literature

Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos [ChIP-seq]

Project description:We performed multi-omics exploration of early aorta endothelial cells (AECs), hemogenic endothelial cells (HECs), pre-HSCs and long-term HSCs (LT-HSCs) along definitive HSC emergence in mouse embryos. Globally, we find that most hematopoiesis related enhancers were already pre-activated at the beginning, followed by strengthened looping structure of enhancers and promoters. After the stronger interactions forming, enhancers can be further activated to promote hematopoiesis gene expressions. Specifically, the important hematopoietic transcription factor (TF) RUNX1 can mediate enhancer-promoter interactions, which starts from a subset of early AECs, prior to appearance of HECs. Thus, the stepwise and asynchrony cooperation of multi-omics and TFs in definitive hematopoiesis has been revealed holistically in vivo. It may also reflect general epigenetic regulation models of developmental processes.

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Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos [Hi-C]

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Data for: A practical guide for analysis of histone post-translational modifications by mass spectrometry: best practices and pitfalls

Project description:Histone proteomics from 5 human cell lines, discussed in publication: "A practical guide for analysis of histone post-translational modifications by mass spectrometry: best practices and pitfalls". Further explanation of data types, methods, and analysis are available in Data Explanation document in the Methods and Protocols folder.

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Chromatin architecture landscape in hierarchical hematopoietic cells

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