Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression

The relationship between cohesin-mediated chromatin looping and gene expression remains unclear. NIPBL and WAPL are two opposing regulators of cohesin activity; depletion of either is associated with changes in both chromatin folding and transcription across a wide range of cell types. However, a direct comparison of their individual and combined effects on gene expression in the same cell type is lacking. We find that NIPBL or WAPL depletion in human HCT116 cells each alter the expression of ~2,000 genes, with only ~30% of the genes shared between the conditions. We find that clusters of differentially expressed genes within the same topologically associated domain (TAD) show coordinated misexpression, suggesting some genomic domains are especially sensitive to either more or less cohesin. Finally, co-depletion of NIPBL and WAPL restores the majority of gene misexpression as compared to either knockdown alone. A similar set of NIPBL-sensitive genes are rescued following CTCF co-depletion. Together, this indicates that altered transcription due to reduced cohesin activity can be functionally offset by removal of either its negative regulator (WAPL) or the physical barriers (CTCF) that restrict loop-extrusion events. PRO-seq was performed for two biological replicates each of a control sample, NIPBL knockdown, WAPL knockdown, CTCF knockdown, NIPBL and WAPL double knockdown, and CTCF and NIPBL double knockdown in the human colorectal cancer cell line, HCT-116 In situ Hi-C was performed for one biological replicate each of control siRNA treated HCT-116 cells. RAD21 and CTCF ChIP-seq were performed in two biological replicates each of HCT-116 cells treated with control siRNA. In situ Hi-C was performed for one biological replicate each of control siRNA treated HCT-116 cells.