{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kierzek E"],"funding":["U.S. Department of Health &amp; Human Services | NIH | Office of Extramural Research, National Institutes of Health","Fundacja na rzecz Nauki Polskiej","NIGMS NIH HHS"],"pagination":["1271"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8917230"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["13(1)"],"pubmed_abstract":["There is increasing interest in the roles of covalently modified nucleotides in RNA. There has been, however, an inability to account for modifications in secondary structure prediction because of a lack of software and thermodynamic parameters. We report the solution for these issues for N<sup>6</sup>-methyladenosine (m<sup>6</sup>A), allowing secondary structure prediction for an alphabet of A, C, G, U, and m<sup>6</sup>A. The RNAstructure software now works with user-defined nucleotide alphabets of any size. We also report a set of nearest neighbor parameters for helices and loops containing m<sup>6</sup>A, using experiments. Interestingly, N<sup>6</sup>-methylation decreases folding stability for adenosines in the middle of a helix, has little effect on folding stability for adenosines at the ends of helices, and increases folding stability for unpaired adenosines stacked on a helix. We demonstrate predictions for an N<sup>6</sup>-methylation-activated protein recognition site from MALAT1 and human transcriptome-wide effects of N<sup>6</sup>-methylation on the probability of adenosine being buried in a helix."],"journal":["Nature communications"],"pubmed_title":["Secondary structure prediction for RNA sequences including N<sup>6</sup>-methyladenosine."],"pmcid":["PMC8917230"],"funding_grant_id":["R01GM076485","UMO-2019/33/B/ST4/01422","R01 GM076485","UMO-2020/01/0/NZ6/00137"],"pubmed_authors":["Watson RM","Kennedy SD","Kierzek E","Zhang X","Szabat M","Kierzek R","Mathews DH"],"additional_accession":[]},"is_claimable":false,"name":"Secondary structure prediction for RNA sequences including N<sup>6</sup>-methyladenosine.","description":"There is increasing interest in the roles of covalently modified nucleotides in RNA. There has been, however, an inability to account for modifications in secondary structure prediction because of a lack of software and thermodynamic parameters. We report the solution for these issues for N<sup>6</sup>-methyladenosine (m<sup>6</sup>A), allowing secondary structure prediction for an alphabet of A, C, G, U, and m<sup>6</sup>A. The RNAstructure software now works with user-defined nucleotide alphabets of any size. We also report a set of nearest neighbor parameters for helices and loops containing m<sup>6</sup>A, using experiments. Interestingly, N<sup>6</sup>-methylation decreases folding stability for adenosines in the middle of a helix, has little effect on folding stability for adenosines at the ends of helices, and increases folding stability for unpaired adenosines stacked on a helix. We demonstrate predictions for an N<sup>6</sup>-methylation-activated protein recognition site from MALAT1 and human transcriptome-wide effects of N<sup>6</sup>-methylation on the probability of adenosine being buried in a helix.","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Mar","modification":"2026-05-09T14:25:06.165Z","creation":"2025-04-06T19:37:01.398Z"},"accession":"S-EPMC8917230","cross_references":{"pubmed":["35277476"],"doi":["10.1038/s41467-022-28817-4"]}}