Abstract Body: Blood pressure (BP)-relevant non-coding SNPs identified by GWAS may influence the expression of distal protein-coding genes. Our previous study detected 195 SNPs (out of 26585) in CTCF-binding sites. CTCF and Cohesin are known to modulate cell-type-specific gene expression from a distance by forming chromatin loops. We hypothesized that both may regulate gene expression in BP-relevant cell types. To test this, we depleted CTCF and Rad21 (Cohesin subunit) in human induced pluripotent stem cells-derived endothelial cells (iEC) and performed genome-wide transcriptomic analysis.
We detected 366 and 4184 differentially expressed genes (DEGs) in CTCF and Rad21 depleted iEC (CTCF-/Rad21-KD-iEC) compared to iEC control, respectively. Among them, 111 DEGs are common between the CTCF-KD and Rad21-KD-iEC, though majority showed opposite regulatory effects (Figure 1A). We found 5619 DEGs in the CTCF-KD vs Rad21-KD-iEC (Figure 1B). Pathway analysis detected elevated cell cycle (G2M checkpoint), DNA replication (E2F targets), and repair pathways in Rad21-KD compared to the CTCF-KD-iEC. Rad21 plays an important role in chromosome partitioning and repair, so its depletion may cause dysregulation of these pathways. While the CTCF-KD-iEC showed enrichment of the Epithelial-to-mesenchymal transition (EMT), inflammatory (IFN-gamma, IFN-alpha), and hypoxia pathways (Figure 1C). As CTCF maintains the chromosome boundaries, CTCF-KD may affect chromatin compactness and trigger abnormal gene expression related to these pathways.
In conclusion, our study detected different effects of depletion of CTCF and Rad21 on gene expression in a BP-relevant cell type. The findings provide a basis to explore the role of chromatin looping in BP-relevant gene regulation.