{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["27(1)"],"submitter":["Li J"],"pubmed_abstract":["Circular RNA (circRNA) represents a critical class of regulatory RNAs with distinctive structural and functional features. The functions of circRNAs are modulated by various RNA modifications. Here, we present CircRM, a nanopore direct RNA sequencing-based computational method for profiling RNA modifications in circRNAs at single-base and single-molecule resolution. By integrating circRNA detection, read-level modification detection, and quantitative assessment of methylation rates, CircRM identified 427 high-confidence circRNAs and enables systematic characterization of three major modifications, m5C (AUC = 0.855), m6A (AUC = 0.817) and m1A (AUC = 0.769). It revealed distinct modification patterns compared with linear RNAs, highlighting RNA-type-specific regulations. We also identified th"],"journal":["Briefings in bioinformatics"],"pagination":["bbaf726"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12798809"],"repository":["biostudies-literature"],"pubmed_title":["CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing."],"pmcid":["PMC12798809"],"pubmed_authors":["Wu Z","Li J","Zhang Y","Wang H","Xia R","Chen S","Meng J"],"additional_accession":[]},"is_claimable":false,"name":"CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.","description":"Circular RNA (circRNA) represents a critical class of regulatory RNAs with distinctive structural and functional features. The functions of circRNAs are modulated by various RNA modifications. Here, we present CircRM, a nanopore direct RNA sequencing-based computational method for profiling RNA modifications in circRNAs at single-base and single-molecule resolution. By integrating circRNA detection, read-level modification detection, and quantitative assessment of methylation rates, CircRM identified 427 high-confidence circRNAs and enables systematic characterization of three major modifications, m5C (AUC = 0.855), m6A (AUC = 0.817) and m1A (AUC = 0.769). It revealed distinct modification patterns compared with linear RNAs, highlighting RNA-type-specific regulations. We also identified th","dates":{"release":"2026-01-01T00:00:00Z","publication":"2026 Jan","modification":"2026-06-10T03:10:06.97Z","creation":"2026-06-10T03:07:16.922Z"},"accession":"S-EPMC12798809","cross_references":{"pubmed":["41529120"],"doi":["10.1093/bib/bbaf726"]}}