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

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. Datasets: 1) Hi-C data of early AECs (E10.0 AGM), HECs (E10.0 AGM), pre-HSCs (E11.0 AGM) and LT-HSCs (E14.5 fetal liver), with replicates. 2) H3K27ac, H3K27me3, H3K4me1, H3K4me3 and RUNX1 ChIP-seq data of early AECs (E10.0 AGM), HECs (E10.0 AGM), pre-HSCs (E11.0 AGM) and LT-HSCs (E14.5 fetal liver), with replicates.