The efficient cleavage of branched DNA intermediates that arise during DNA replication, recombination or repair is essential for the maintenance of genomic stability. Human SLX4 is a scaffold protein for the assembly and activation of three structure selective endonucleases (SSEs) that cleave branched DNA structures - SLX1, MUS81-EME1 and XPF-ERCC1 (collectively known as the SMX complex). These endonucleases have diverse substrate specificities and play multiple individual and combined roles in DNA metabolism.

SLX4 interacts with MutSβ (MSH2-MSH3), a heterodimeric ATPase that binds to heteroduplex DNA loops and other branched DNA structures. MutSβ is required for the mismatch repair (MMR) of small loops that arise erroneously during replication. MutSβ also has a pathogenic role in promoting the instability of trinucleotide repeat tracts, a process causative of numerous degenerative disorders such as Huntington’s disease and myotonic dystrophy. However, little is known about the function of SLX4-MutSβ complexes or how they contribute to genomic stability.

Here we show that SLX4 interacts with MutSβ in human cells in the absence of exogenous DNA damage. In vitro, purified MutSβ stimulates the SLX1-SLX4 and SMX-mediated cleavage of branched DNA structures similar to those associated with trinucleotide repeat instability and homologous recombination. Moreover, MutSβ is required for the efficient processing of late recombination intermediates in cells to allow accurate sister chromatid separation. We propose that MutSβ is an important component of the SLX4-repair complex, and depending on the DNA context, SLX4-MutSβ interactions can function to either protect genome integrity, or promote genomic instability.