FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington’s disease

CAG repeat expansion in the HTT gene drives Huntington’s disease (HD) pathogenesis and is modulated by DNA damage repair pathways. In this context, the interaction between FAN1, a DNA-structure-specific nuclease, and MLH1, member of the DNA mismatch repair pathway (MMR), is not defined. Here, we identify a highly conserved SPYF motif at the N terminus of FAN1 that binds to MLH1. Our data support a model where FAN1 has two distinct functions to stabilize CAG repeats. On one hand, it binds MLH1 to restrict its recruitment by MSH3, thus inhibiting the assembly of a functional MMR complex that would otherwise promote CAG repeat expansion. On the other hand, it promotes accurate repair via its nuclease activity. These data highlight a potential avenue for HD therapeutics in attenuating somatic expansion. [Display omitted] •FAN1 binds MLH1 via conserved 126SPYF129 residues, acting as a canonical MIP-box•FAN1-MLH1 binding regulates mismatch repair activity and complex formation•FAN1-MLH1 binding regulates the HTT CAG expansion rate FAN1 modifies Huntington’s disease pathogenesis, but the mechanism has remained elusive. Goold et al. demonstrate that FAN1 binds MLH1 through residues 126SPYF129, competing with MSH3, and sequesters MLH1 from the mismatch repair pathway. In turn, this reduces mismatch repair activity and suppresses expansion of the pathogenic HTT CAG trinucleotide repeat.