[The three-dimensional chromatin architecture plays a critical role in the establishment of cell-type-specific gene regulatory networks in eukaryotic cells. How pluripotent stem cells (PSC) alter their chromatin architecture to direct cell fate specification remains to be elucidated. Here, using a human PSC cardiomyocyte differentiation model, we analyze the dynamic reorganization of chromatin structure and gene regulatory networks during key transitional stages of cardiomyocyte development. We show that many human PSC-specific topologically associating domains (TADs) are driven by active transcription of the primate-specific retroviruses HERVH. These HERVH are silenced at the earliest stages of differentiation , accompanied by loss of TAD borders and subsequent merging of cognate TADs during differentiation, which leads to repression of gene expression within these domains . In line with these findings, deletion of select HERVHs results in elimination of corresponding TAD boundaries in human PSCs. We further discovered developmental stage-specific chromatin loop interactions that predict target genes of cardiac-related trait/disease non-coding genetic variants. Overall, our results not only highlight a novel role for endogenous retroviruses in shaping species-specific PSC chromatin architecture during evolution but also provide a genomic blueprint for understanding the impact of non-coding variants in congenital and adult heart disease/traits.]
