CTCF prevents genomic instability by promoting homologous recombination-directed DNA double-strand break repair

Abstract

CTCF is an essential epigenetic regulator mediating chromatin insulation, long-range regulatory interactions, and the organization of large topological domains in the nucleus. Phenotypes of CTCF haploinsufficient mutations in humans, knockout in mice, and depletion in cells are often consistent with impaired genome stability, but a role of CTCF in genome maintenance has not been fully investigated. Here, we report that CTCF maintains genome stability, is recruited to sites of DNA damage, and promotes homologous recombination repair of DNA double-strand breaks (DSBs). CTCF depletion increased chromosomal instability, marked by chromosome breakage and end fusions, elevated genotoxic stress-induced genomic DNA fragmentation, and activated the ataxia telangiectasia mutated (ATM) kinase. We show that CTCF could be recruited to drug-induced 53BP1 foci and known fragile sites, as well as to I-SceI endonuclease-induced DSBs. Laser irradiation analysis revealed that this recruitment depends on ATM, Nijmegen breakage syndrome (NBS), and the zinc finger DNA-binding domain of CTCF. We demonstrate that CTCF knockdown impaired homologous recombination (HR) repair of DSBs. Consistent with this, CTCF knockdown reduced the formation of γ-radiation-induced Rad51 foci, as well as the recruitment of Rad51 to laser-irradiated sites of DNA lesions and to I-SceI-induced DSBs. We further show that CTCF is associated with DNA HR repair factors MDC1 and AGO2, and directly interacts with Rad51 via its C terminus. These analyses establish a direct, functional role of CTCF in DNA repair and provide a potential link between genome organization and genome stability.CTCF | chromatin | genome stability | DNA repair | homologous recombination

Nucleotide Excision Repair and Transcription‐Associated Genome Instability

“…Abrogation of ERCC1 in Ercc1 −/− mice or exposure of primary embryonic fibroblasts to the DNA interstrand cross‐linker mitomycin triggers the localization of CTCF to heterochromatin and the dissociation of the CTCF–cohesin complex and ATRX from promoters and imprinted control regions. These findings are also in agreement with the newly identified role for CTCF in facilitating the repair of DNA DSBs through HR . CTCF also interacts with CSB .…”

Radiation-Induced DNA Damage and Repair Effects on 3D Genome Organization

“…This suggests that changes in the structure of local genome domains may happen at a broader scale after IR. Additionally, CCCTC-binding factor (CTCF) and cohesin have been shown to be early responders to DNA damage induced by IR 17,18,19,20 . These proteins have also been recently demonstrated to play significant roles in chromosome folding 21,22,23,24 , contributing to the formation of topologically associating domains (TADs).…”

Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer

“…TADs also function as structural domains to constrain long‐range contacts between enhancers and promoters such that they occur almost exclusively within TADs . Given the inextricable link between structure and function within the context of the cell nucleus, it is important to consider the role of HCO in maintaining genomic stability and fidelity and the resulting disruptions that occur in these TAD microenvironments introduced by translocations, deletions, inversions, and mutations during cancer progression (Figure ) …”