Reprogramming of 3D genome structure underlying HSPC development in zebrafish

Autor: Min He, Xiaoli Li, Bingxiang Xu, Yinbo Lu, Jingyi Lai, Yiming Ling, Huakai Liu, Ziyang An, Wenqing Zhang, Feifei Li
Jazyk: angličtina
Rok vydání: 2024
Předmět:
Zdroj: Stem Cell Research & Therapy, Vol 15, Iss 1, Pp 1-17 (2024)
Druh dokumentu: article
ISSN: 1757-6512
DOI: 10.1186/s13287-024-03798-x
Popis: Abstract Background Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals. Understanding the mechanism underlying HSPC development is a holy grail of hematopoietic biology, which is helpful for HSPC clinical application. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision; however, its dynamic and role in HSPC development is poorly investigated. Methods We performed chromatin structure and multi-omics dissection across different stages of HSPC developmental trajectory in zebrafish for the first time, including Hi-C, RNA-seq, ATAC-seq, H3K4me3 and H3K27ac ChIP-seq. Results The chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure. We revealed the multi-scale reorganization of chromatin structure and its influence on transcriptional regulation and transition of cell fate during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably, PU.1 was identified as a potential factor mediating formation of promoter-involved loops and regulating gene expression of HSPC. Conclusions Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factors involved in HSPC chromatin interactions, which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision.
Databáze: Directory of Open Access Journals
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