Resolution of sequence divergence for repeat-mediated deletions shows 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 sequence divergence 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 break. We found that the mismatch repair factor MLH1 suppresses RMDs with sequence divergence in the same pathway as 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 the resolution of sequence divergence in the RMD product has a specific polarity, where divergent bases that are proximal to the chromosomal break end are preferentially removed. Moreover, we found that the domain of MLH1 that forms part of the MLH1-PMS2 endonuclease is important for polarity of resolution of sequence divergence. We also identified distinctions between MLH1 versus TOP3α in regulation of RMDs. We suggest that MLH1 suppresses RMDs with sequence divergence, while also promoting directional resolution of sequence divergence in the RMD product.

Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing in Saccharomyces cerevisiae

“…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 [ 41 ]. Another recent study by Trost et al [ 42 ] 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.…”

“…In yeast, Mlh1 and Pms1 are needed for mismatch correction per se but showed no effect on heteroduplex rejection in SSA. Trost et al also examined the bias in repair when one nonhomologous tail was 268 nt long and the other varied from 16 nt to 9100 nt [ 42 ]. Longer tails impaired SSA both for perfectly matched 267-bp repeats or for 1–3% divergent sequences.…”

Prognostic value of SLC4A4 and its correlation with the microsatellite instability in colorectal cancer

“…MSI is a feature of many disorders, most of which are neoplastic, with Lynch syndrome being the most well-known non-neoplastic disorder. Protein dysfunction in the MMR family is involved in the occurrence of Lynch syndrome, with most families diagnosed with Lynch syndrome having MLH1 and MSH2 mutations, some families having MSH6 mutations, and a few families having PMS2 mutations ( 29 ). The occurrence of Lynch syndrome and partial sporadic colorectal cancer is not related to oncogene activation and tumor suppressor gene inactivation, rather it is caused by MSI due to mutations in mismatch repair genes ( 30 ).…”

Functions of PMS2 and MLH1 important for regulation of divergent repeat-mediated deletions

“…This annealing causes the formation of 3' nonhomologous tails which are removed prior to ligation, resulting in an RMD [10]. Since RMDs are inherently mutagenic, several pathways appear to suppress these events [1,2,[10][11][12]. In particular, RMDs between divergent repeats are prone to heteroduplex rejection mechanisms via the DNA mismatch repair (MMR) pathway, and the BLM/TOP3a/ RMI1/RMI2 complex [13][14][15][16].…”