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While searching for germline mutations inMLH1 and MSH2mismatch repair genes in patients affected with hereditary non-polyposis colorectal cancer (HNPCC), we have observed that human chromosome 3 carries two main haplotypes of the housekeeping geneMLH1. This so called caretaker gene acts as a major guardian of the genome,1 and cells in whichMLH1 is inactivated develop a characteristic mutator phenotype, as a result of a default in post-replicative DNA mismatch repair.2 3 In humans, the protein encoded byMLH1 forms at least two dimeric factors with either PMS2 orMLH3.4-6 Germline defects inMLH1 account for a number of sporadic epithelial cancers and for the majority of cases of HNPCC,7 which is the most common form of all familial cancers along with breast cancer. In addition to its role in DNA editing, the multifunctional MLH1 gene is thought to participate in mitotic and meiotic recombination,8 as well as in apoptosis.9 InE coli, evidence has accumulated to suggest that MLH1 MutL homologue may behave as a “molecular matchmaker” by acting as a chaperone, which facilitates the conformational changes required to assemble a DNA repair proficient complex from its individual components.10 In yeast, studies on segregation data of all genes known to participate in mismatch repair have shown that the MLH1gene plays a predominant role in promoting crossing over,11 and at least in mice, the MLH1 protein appears to be a component of the late replication nodules that probably prevent non-homologous genetic recombination between homeologous sequences.8 During chromosome pairing in meiosis I, the protein foci allow even better mapping of crossover events and interference distances than using chiasmata.12 Our data suggest that two major haplotypes spanning at least 55 kb of theMLH1 gene, completely …