Mismatch resolution for repeat-mediated deletions show a polarity that is mediated by MLH1

Abstract

Repeat-mediated deletions (RMDs) are a type of chromosomal rearrangement between two homologous sequences that causes loss of the sequence between the repeats, along with one of the repeats. Sequence divergence between repeats suppresses RMDs; the mechanisms of such suppression and of resolution of the mismatched bases remains poorly understood. We identified RMD regulators using a set of reporter assays in mouse cells that test two key parameters: repeat sequence divergence and the distances between one repeat and the initiating chromosomal double-strand break. We found that the mismatch repair factor MLH1 suppresses RMDs with sequence divergence in a manner that is epistatic with the mismatch repair factors MSH2 and MSH6, and which is dependent on residues in MLH1 and its binding partner PMS2 that are important for nuclease activity. Additionally, we found that resolution of mismatches in the RMD product have a specific polarity, where mismatched bases that are proximal to the chromosomal break end are preferentially removed. Moreover, we found that the MLH1 endonuclease domain is important for this polarity of mismatch resolution. Finally, we identified distinctions between MLH1 vs. TOP3α in regulation of RMDs. We suggest that MLH1 suppresses RMDs with sequence divergence, while also promoting directional mismatch resolution.

Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing inSaccharomyces cerevisisae

“…In a model with a single mismatch in a 152-bp segment, SSA events exhibited a modest 60-80% bias in correcting the mismatch prompted by the shorter of the two nonhomologous tails (33 nt vs. 11 nt) and that the pattern is reversed when cleavage creates tails of 0 and 42 nt [36]. Another recent study by Trost et al [37] found that mismatches proximal to a nonhomologous tail were preferentially removed. However, unlike in budding yeast, Mlh1 as well as Msh6 caused a reduction in SSA outcomes with mismatched substrates.…”

“…Another recent study by Trost et al [37] found that mismatches proximal to a nonhomologous tail were preferentially removed. However, unlike in budding yeast, Mlh1 as well as Msh6 caused a reduction in SSA outcomes with mismatched substrates.…”