biostudies-literatureUnknown27(1)Li JCircular 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 thBriefings in bioinformaticsbbaf726https://www.ebi.ac.uk/biostudies/studies/S-EPMC12798809biostudies-literatureCircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.PMC12798809Wu ZLi JZhang YWang HXia RChen SMeng JfalseCircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.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 th2026-01-01T00:00:00Z2026 Jan2026-06-10T03:10:06.97Z2026-06-10T03:07:16.922ZS-EPMC127988094152912010.1093/bib/bbaf726