CHD-associated enhancers direct human cardiomyocyte lineage commitment.

Enhancers orchestrate gene expression programs that drive multicellular development and lineage commitment. Thus, genetic variants at enhancers are thought to contribute to developmental diseases by altering cell fate commitment. However, while many variant-containing enhancers have been identified, systematic studies to endogenously test the impact of these enhancers on lineage commitment have been lacking. We performed a single-cell CRISPRi screen to directly assess the roles of 25 enhancers and putative cardiac target genes implicated in genetic studies of congenital heart defects (CHD). We identified 16 enhancers whose repression leads to delayed differentiation of human cardiomyocytes. A focused analysis on 6 TBX5 enhancers showed that TBX5 enhancer perturbation delays the transcriptional switch from mid-CM to late-CM states. Knockout of two TBX5 enhancers resulted in X and Y, which phenocopy expected CHD phenotypes. Together, these results identify critical enhancers of cardiac development and suggest that misregulation of these enhancers could contribute to cardiac defects in human patients. Overall design: Single cell sequencing of differentiated cardiomyocytes from H9 hESC comprised of three separate conditions. Large screen lentivirally transduced hESCs, validation screen lentivirally transduced hESCs, and hESCs in which either a TBX5 enhancer or the TBX5 promoter were knocked out.