ArticleBriefings in bioinformatics2026
CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.
Article in Briefings in bioinformatics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Diagnostic and prognostic role of circular RNAs: Analytical challenges and emerging opportunities.iScience · 2026Review
- Sequence determinant and functional relevance of 8-oxoguanine RNA modification unveiled from foundation-model-based predictor.Molecular therapy. Nucleic acids · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Addressing biases and limitations in feature attribution for circRNA modification profiling.Briefings in bioinformatics · 2026Article
- Experimental and Computational Tools for Mapping Circular RNA Modifications.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
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 the key features of circRNA-specific modifications, such as the enrichment near the back-splice junctions. Cross-cell line analyses further demonstrated conserved and cell-type-specific modification patterns. Together, these findings reveal, at the computational level, a unique epitranscriptomic landscape associated with circRNAs and establish CircRM as a powerful tool for advancing the study of RNA modifications in circular RNA biology. CircRM is free accessible at: https://github.com/jiayiAnnie17/CircRM.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.