PI/Associated Prof. Sun Yat-sen University Guangzhou, Guangdong, China
Abstract: Embryonic stem cells (ESCs) undergo fate transitions in response to external signaling stimuli, a process dependent on precise expression of the specific genes; however, the intrinsic regulatory mechanisms involved in this process remain largely unknown. Here, we integrated bulk RNA sequencing, single-cell RNA sequencing (scRNA-seq), 4D-SmartDIA quantitative proteomics and retinoic acid (RA) receptor deletion modeling to demonstrate that RA signaling-induced early ESC differentiation is characterized by a multi-lineage process, with Cyp26 and Hoxb cluster genes identified as its key targets. RA signaling activation leads to the emergence of RA-induced enhancers (RAiEs) in proximal/distal regions of the cluster gene loci, while inhibiting RA signaling markedly decreases the activity and chromatin accessibility of these RAiEs. Mechanistically, we found that RAiEs form specific chromatin loops with cluster gene loci upon RA induction, whereas these chromatin interactions are significantly reduced in RARs knockout cells. Deletion of proximal/distal RAiEs suppressed cluster gene expression, thereby disrupting ESC differentiation. Our results reveal a critical mechanism that highlights the importance of the specific 3D chromatin structure of RAiEs in regulating cluster gene expression and ESC fate transitions.
