{"doi":"10.5281/zenodo.10498510","title":"Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing in Saccharomyces cerevisiae","abstract":"We have studied deletion formation by single-strand annealing (SSA) between naturally divergent 200 bp repeats in budding yeast. SSA was initiated by creating a site-specific double-strand break (DSB) in the region between the two repeats, either using HO endonuclease or guide RNA-directed Cas9. In this process, the ends are resected 5’ to 3’, leaving long 3’-ended single-stranded sequences that can anneal. After annealing any 3’-ended nonhomologous tails are clipped off by the Rad1-Rad10 endonuclease. The presence of nonhomologous tails triggers a Msh2-Msh3-dependent and Sgs1-dependent heteroduplex rejection when there are 7 heterologies within the 200-bp repeats being annealed, whereas a “tailless” construct is not rejected. Mismatch repair within the heteroduplex is Msh2-Msh6-dependent; however, a msh2 deletion proved have a spectrum of mismatch repair different from a msh3 msh6 double mutant, implying that Msh2 may have some additional role when the intermediates have nonhomologous 3’ tails. “Tailed” repeats yielded a gradient of repair that favored sequences in the “left” repeat, but “Tailless” SSA yielded a uniform correction of all 7 heterologies in the 200-bp region. A cluster of repeats near the left end of the sequence provokes correction of these markers in a Msh6-independent fashion; this correction is not attributable to 3’ to 5’ exonuclease activity of DNA polymerase d and may reflect instances where part of the homologous sequence itself is clipped off by the Ra1-Rad10 endonuclease. The presence or absence of nonhomologous tails also affected the requirement for the Rad52 strand annealing protein. Both in the chromosomal SSA assay and in a plasmid assay, Rad52 was largely dispensable when there were no nonhomologous tails after strand annealing.","journal":"Zenodo (CERN European Organization for Nuclear Research)","year":2024,"id":496194,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9623,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":793952,"name":"Neal Sugawara","orcid":"0009-0009-0495-9618","position":1,"is_corresponding":false},{"id":13520,"name":"James E. Haber","orcid":"0000-0002-1878-0610","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:09:23.333150Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}