Role of CTCF in Nucleotide Excision Repair

/ABSTRACT Nucleotide excision repair (NER) is a conserved and versatile DNA repair pathway that maintains genome stability by removing helix-distorting and bulky DNA lesions caused by a variety of DNA damaging agents such as ultraviolet (UV) radiation, polyaromatic hydrocarbons and cisplatin. Defects in NER are associated with severe human disorders, such as xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). The CCCTC-binding factor (CTCF) is a master regulator of three-dimensional (3D) genome architecture and has been implicated in the cellular response to DNA damage and repair, including the DNA double-strand break (DSB) repair pathway. However, its specific role in NER remains unexplored. Despite extensive studies on the core biochemical mechanisms of NER, little is known about how this repair process operates within the complex 3D genome organization in living cells. The objective of this proposal is to elucidate the mechanisms by which CTCF facilitates NER in the context of 3D genome organization. The central hypothesis is that CTCF promotes efficient NER by (1) directly interacting with NER proteins at damage sites, (2) reorganizing chromatin structure to facilitate repair, and (3) modulating chromatin accessibility in response to DNA damage. To test this hypothesis, we will pursue three specific aims: (1) to determine CTCF's involvement in the two NER subpathways and identify its interactions with NER proteins; (2) to delineate the role of CTCF-mediated 3D genome reorganization in NER; and (3) to investigate the role of CTCF-mediated modulation of chromatin accessibility in NER. These complementary aims will be accomplished by using a multi-disciplinary approach that integrates cutting-edge techniques in genome editing, DNA damage and repair mapping, proteomics, 3D genomics, and bioinformatics. The proposed research is significant because it will (1) establish a paradigm for investigating the role of CTCF in NER, paving the way for future studies on how NER functions within the complex nuclear architecture; (2) provide novel insights into the complex interplay between 3D genome structure, DNA damage formation, and NER; (3) develop integrative multi-omics and bioinformatics approaches which will provide a foundation for studying the roles of other chromatin organizers in various DNA repair pathways and their potential dysregulation in disorders associated with genome instability. The project is innovative as it represents a substantial departure from the traditional biochemical view of NER by comprehensively investigating how NER functions within the complex 3D nuclear architecture in living cells. Project Number: 1R01GM159028-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Wentao Li | Institution: UNIVERSITY OF GEORGIA, ATHENS, GA | Award Amount: $300,872 | Activity Code: R01 | Study Section: Molecular Genetics Study Section[MG] View on NIH RePORTER: https://reporter.nih.gov/project-details/11298358