{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Schnable BL"],"funding":["U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences","U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)","NIEHS NIH HHS","U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences","NCI NIH HHS","U.S. Department of Health & Human Services | NIH | NIH Office of the Director","NIGMS NIH HHS","U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)","U.S. Department of Health & Human Services | NIH | NIH Office of the Director (OD)","NIH HHS"],"pagination":["9226"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11512004"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["15(1)"],"pubmed_abstract":["Base excision repair is the main pathway involved in active DNA demethylation. 5-formylcytosine and 5-carboxylcytosine, two oxidized moieties of methylated cytosine, are recognized and removed by thymine DNA glycosylase (TDG) to generate an abasic site. Using single molecule fluorescence experiments, we study TDG in the presence and absence of 5-formylcytosine. TDG exhibits multiple modes of linear diffusion, including hopping and sliding, in search of base modifications. TDG active site variants and truncated N-terminus, reveals these variants alter base modification search and recognition mechanism of TDG. On DNA containing an undamaged nucleosome, TDG is found to either bypass, colocalize with, or encounter but not bypass the nucleosome. Truncating the N-terminus reduces the number of i"],"journal":["Nature communications"],"pubmed_title":["Thymine DNA glycosylase combines sliding, hopping, and nucleosome interactions to efficiently search for 5-formylcytosine."],"pmcid":["PMC11512004"],"funding_grant_id":["R35 GM136225","F32 ES034982","R35 GM128562","R35-GM136225","R35GM128562","S10 OD032158","F32GM140718","S10OD032158-01A1","P30 CA047904","T32GM088119","T32 GM088119","R35 ES031638","F32ES034982","R35ES031638","F32 GM140718"],"pubmed_authors":["Schaich MA","Drohat AC","Leary LP","Schnable BL","Roginskaya V","Freudenthal BD","Weaver TM","Van Houten B"],"additional_accession":[]},"is_claimable":false,"name":"Thymine DNA glycosylase combines sliding, hopping, and nucleosome interactions to efficiently search for 5-formylcytosine.","description":"Base excision repair is the main pathway involved in active DNA demethylation. 5-formylcytosine and 5-carboxylcytosine, two oxidized moieties of methylated cytosine, are recognized and removed by thymine DNA glycosylase (TDG) to generate an abasic site. Using single molecule fluorescence experiments, we study TDG in the presence and absence of 5-formylcytosine. TDG exhibits multiple modes of linear diffusion, including hopping and sliding, in search of base modifications. TDG active site variants and truncated N-terminus, reveals these variants alter base modification search and recognition mechanism of TDG. On DNA containing an undamaged nucleosome, TDG is found to either bypass, colocalize with, or encounter but not bypass the nucleosome. Truncating the N-terminus reduces the number of i","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Oct","modification":"2026-06-02T04:56:33.409Z","creation":"2025-04-04T00:29:25.262Z"},"accession":"S-EPMC11512004","cross_references":{"pubmed":["39455577"],"doi":["10.1038/s41467-024-53497-7"]}}