Molecular systems that modulate nucleic acid repeat instabilities

The National Institute of General Medical Sciences awarded Thomas Jefferson University $246,999 on June 1, 2026, as a Project Grant (CFDA 93.859, Biomedical Research and Research Training) to support research into molecular systems that modulate nucleic acid repeat instabilities.

The research addresses how repetitive DNA sequences—which constitute approximately 50 percent of the human genome and are prone to length polymorphisms—undergo expansion at rates 101–105 fold higher than other mutation types. The work focuses on understanding the molecular mechanisms by which the FAN1 deoxyribonuclease suppresses triplet repeat expansion, a process relevant to neurodegenerative diseases including Huntington's disease, Friedreich's ataxia, and Fragile X-related disorders. Using biochemical, cellular, and structural approaches, the investigator team discovered a novel nuclease function for FAN1 that cleaves triplet repeat extrahelical extrusions through activation by the sliding clamp PCNA, leading to removal of extrusions via short-patch excision and repair. The research will examine the activities and molecular mechanisms involved in FAN1-dependent extrusion repair, assess whether FAN1 plays a global role in genome-wide stability of short tandem repeats, and determine functional consequences of FAN1 mutations.

Performance occurs at Thomas Jefferson University's Philadelphia, Pennsylvania facility. The award period runs through March 31, 2031.

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.