{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T03:46:50Z","timestamp":1775965610439,"version":"3.50.1"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T00:00:00Z","timestamp":1768262400000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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\u2009=\u20090.855), m6A (AUC\u2009=\u20090.817) and m1A (AUC\u2009=\u20090.769). 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.<\/jats:p>","DOI":"10.1093\/bib\/bbaf726","type":"journal-article","created":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T13:04:04Z","timestamp":1766581444000},"source":"Crossref","is-referenced-by-count":1,"title":["CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing"],"prefix":"10.1093","volume":"27","author":[{"given":"Jiayi","family":"Li","sequence":"first","affiliation":[{"name":"Department of Biosciences and Bioinformatics, School of Science, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Center for Intelligent RNA Therapeutics, Suzhou Key Laboratory of Cancer Biology and Chronic Disease, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool , Biosciences Building, Crown Street, Liverpool L69 7ZB ,","place":["United Kingdom"]}]},{"given":"Shenglun","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioinformatics, School of Science, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Center for Intelligent RNA Therapeutics, Suzhou Key Laboratory of Cancer Biology and Chronic Disease, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Leahurst Campus, Neston, Brownlow Hill, Wirral CH64 7TE ,","place":["United Kingdom"]}]},{"given":"Zhixing","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioinformatics, School of Science, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Center for Intelligent RNA Therapeutics, Suzhou Key Laboratory of Cancer Biology and Chronic Disease, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"The School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang), Xi\u2019an Jiaotong-Liverpool University , 5th Floor, Building D, No. 111 Road, Taicang Avenue, Taicang, Suzhou, Jiangsu 215400 ,","place":["China"]},{"name":"Department of Computer Science, University of Liverpool , Ashton Building, Liverpool, Merseyside L69 3DR ,","place":["United Kingdom"]}]},{"given":"Haozhe","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioinformatics, School of Science, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Center for Intelligent RNA Therapeutics, Suzhou Key Laboratory of Cancer Biology and Chronic Disease, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Department of Computer Science, University of Liverpool , Ashton Building, Liverpool, Merseyside L69 3DR ,","place":["United Kingdom"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6167-4234","authenticated-orcid":false,"given":"Rong","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioinformatics, School of Science, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Center for Intelligent RNA Therapeutics, Suzhou Key Laboratory of Cancer Biology and Chronic Disease, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"The School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang) , Xi\u2019an Jiaotong-Liverpool University, 5th Floor, Building D, No. 111 Road, Taicang Avenue, Taicang, Suzhou, Jiangsu 215400 ,","place":["China"]},{"name":"Department of Computer Science, University of Liverpool , Ashton Building, Liverpool, Merseyside L69 3DR ,","place":["United Kingdom"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3455-205X","authenticated-orcid":false,"given":"Jia","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioinformatics, School of Science, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Center for Intelligent RNA Therapeutics, Suzhou Key Laboratory of Cancer Biology and Chronic Disease, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool , Biosciences Building, Crown Street, Liverpool L69 7ZB ,","place":["United Kingdom"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1900-6712","authenticated-orcid":false,"given":"Yuxin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioinformatics, School of Science, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Center for Intelligent RNA Therapeutics, Suzhou Key Laboratory of Cancer Biology and Chronic Disease, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123 ,","place":["China"]},{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool , Biosciences Building, Crown Street, Liverpool L69 7ZB ,","place":["United Kingdom"]},{"name":"State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences , No. 15 Datun Road, Chaoyang District, Beijing 100101 ,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2026,1,13]]},"reference":[{"key":"2026011313105161900_ref1","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1038\/s41587-021-00842-6","article-title":"Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long","volume":"39","author":"Zhang","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2026011313105161900_ref2","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1038\/nbt.2890","article-title":"Detecting and characterizing circular RNAs","volume":"32","author":"Jeck","year":"2014","journal-title":"Nat 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