CCCTC binding factor (CTCF) has been implicated in mediating chromatin insulation and long-distance interactions between enhancer and promoter. In this study, to study the roles of CTCF in somatic cell reprogramming, we performed RNA-seq, Hi-C, ChIP-seq and ATAC-seq at the specific stage of reprogramming. Through bioinformatics analysis, our data indicated that CTCF promotes enhancer-promoter interactions and chromatin accessibility to regulate the expression of key pluripotency genes; meanwhile, it serves as an insulator to suppress the expression of key somatic genes. Smarca5 loss inhibits CTCF-promoted reprogramming by reversing CTCF insulator activity on MEF-specific genes and leading to incorrect nucleosome positioning adjacent to CTCF binding sites. These findings reveal the dual functions of CTCF as both a structural regulator and insulator in conjunction with a key chromatin remodeler to drive cellular reprogramming towards pluripotency.
Examination of chromatin interactions in mouse embryonic fibroblast (MEF) and OSKM reprogrammed cells on day 10. Examination of chromatin interactions in reprogramming cells with OSKM plus control, OSKM plus Ctcf overexpression and OSKM with Ctcf overexpression plus Smarca5 knockdown, reprogramming cells with OSKM plus control or Ctcf shRNA on day 10. Examination of chromatin interactions in sorted reprogramming intermediate cells in the TetOn lentivirus OSKM reprogramming system with both control shRNA and Ctcf knockdown by BL-Hi-C deep sequencing.