DNA methyltransferase Dnmt3ba-mediated epigenetic modulation of Integrin signaling is essential for hematopoietic stem and progenitor cell development

In vertebrate embryonic development, hematopoietic stem and progenitor cells (HSPCs) originate from a subset of arterial endothelial cells in the ventral wall of the dorsal aorta through endothelial-to-hematopoietic transition (EHT). Despite extensive research efforts, gaps persist in understanding the establishment of EHT and HSPC generation. In this study, we demonstrate that DNA methyltransferase 3ba (Dnmt3ba), highly expressed in the hemogenic endothelial cells (HECs), plays a crucial role in HEC generation and HSPC development. Depletion of Dnmt3ba impairs HEC survival, which ultimately affects the generation and differentiation of HSPCs in zebrafish. Mechanistically, Dnmt3ba deficiency leads to hypomethylation at the itgα3b and itgα7 loci, diminishing the expression of these Integrins and downstream Akt signaling and Mdm2 phosphorylation, while concurrently triggering HEC apoptosis by upregulation of P53 activity. Manipulation of DNMT3B in an iPSC-derived human hematopoietic differentiation system indicates functional conservation. Collectively, our findings unveil an epigenetic mechanism governed by Dnmt3ba, orchestrating HEC survival through epigenetic modulation of Integrin signaling. Whole-genome bisulfite sequencing (WGBS) and RNA-seq were performed on hematopoietic endothelial cells (HECs) isolated from Danio rerio embryos at 36 hours post-fertilization (hpf). For each experiment, the number of embryos in each group was determined based on the amount required to obtain sufficient RNA or DNA from approximately 5,000 cells for RNA-seq and WGBS, respectively. Three biological replicates were prepared for both the control and dnmt3ba morphant groups. All samples that met the quality and quantity requirements were included in the sequencing analysis.