Molecular systems that modulate nucleic acid repeat instabilities

/Abstract Repetitive DNA sequences constitute approximately 50% of the human genome and tend to be polymorphic in length due to their genetic instability. These length changes occur at 101-105 fold higher rates than other types of mutations due to the formation of transient unusual DNA structures (extrahelical extrusions) during DNA metabolic processes. The importance of DNA repeat instability is underscored by the fact that several neurodegenerative diseases, such as Huntington’s disease, Friedreich’s ataxia, and Fragile X-related disorders are caused by expansion of triplet repeat elements in distinct and unrelated genes. Therefore, the long-term goal of our research is to understand the molecular mechanisms that modulate DNA repeat expansion. Genetic studies have identified FAN1 (a deoxyribonuclease that was originally described as a DNA interstrand crosslink repair enzyme) as a suppressor of triplet repeat expansion, although the molecular mechanisms underlying this process are not understood. Using biochemical, cellular, and structural approaches, we discovered a novel function for FAN1 as a nuclease that cleaves triplet repeat extrahelical extrusions by a process that requires activation by the sliding clamp PCNA. This cleavage leads to removal of the extrusion by a short-patch excision/repair process using activities that have not yet been identified. Our findings lay the foundations for understanding how FAN1 suppresses repeat expansion. Our work also provides a springboard to address the following broad questions about the role of FAN1 as a general guardian of genetic information. (i) What are the activities involved in the FAN1-dependent extrusion repair process, and by what molecular mechanisms they function? (ii) Does FAN1 play a global role as a DNA repair system that broadly maintains the genome-wide stability of short tandem repeats? (iii) What are the functional consequences of protein-protein interactions that mediate crosstalk between FAN1 activities and DNA mismatch repair (a highly conserved anti-mutagenic DNA repair pathway that plays a counterintuitive mutagenic role in triplet repeat expansion)? Our proposed studies will enable us to integrate multidisciplinary approaches and develop a unified understanding of the mechanisms and interplay of DNA repair pathways in maintaining genome stability. Project Number: 1R35GM164179-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Anna Pluciennik | Institution: THOMAS JEFFERSON UNIVERSITY, PHILADELPHIA, PA | Award Amount: $246,999 | Activity Code: R35 | Study Section: Special Emphasis Panel[ZRG1 MGG-D (55)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11333956