{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T04:00:51Z","timestamp":1773288051853,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2022,6,1]],"date-time":"2022-06-01T00:00:00Z","timestamp":1654041600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81870129"],"award-info":[{"award-number":["81870129"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82170170"],"award-info":[{"award-number":["82170170"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82173314"],"award-info":[{"award-number":["82173314"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Circular ribonucleic acids (RNAs) (circRNAs) are formed by covalently linking the downstream splice donor and the upstream splice acceptor. One of the most important functions of circRNAs is mainly exerted through binding RNA-binding proteins (RBPs). However, there is no efficient algorithm for identifying genome-wide circRNA\u2013RBP interactions. Here, we developed a unique algorithm, circRIP, for identifying circRNA\u2013RBP interactions from RNA immunoprecipitation sequencing (RIP-Seq) data. A simulation test demonstrated the sensitivity and specificity of circRIP. By applying circRIP, we identified 95 IGF2BP3-binding circRNAs based on the IGF2BP3 RIP-Seq dataset. We further identified 2823 and 1333 circRNAs binding to &amp;gt;100 RBPs in K562 and HepG2 cell lines, respectively, based on enhanced cross-linking immunoprecipitation (eCLIP) data, demonstrating the significance to survey the potential interactions between circRNAs and RBPs. In this study, we provide an accurate and sensitive tool, circRIP (https:\/\/github.com\/bioinfolabwhu\/circRIP), to systematically identify RBP and circRNA interactions from RIP-Seq and eCLIP data, which can significantly benefit the research community for the functional exploration of circRNAs.<\/jats:p>","DOI":"10.1093\/bib\/bbac186","type":"journal-article","created":{"date-parts":[[2022,4,25]],"date-time":"2022-04-25T11:13:26Z","timestamp":1650885206000},"source":"Crossref","is-referenced-by-count":22,"title":["circRIP: an accurate tool for identifying circRNA\u2013RBP interactions"],"prefix":"10.1093","volume":"23","author":[{"given":"Xin","family":"Dong","sequence":"first","affiliation":[{"name":"School of Basic Medical Sciences, Wuhan University , Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Urology,Tongji Hospital, Tongji Medical College,Huazhong University of Science and Technology , 430030, Wuhan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenbo","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Wuhan University , Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Wuhan University , Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liuping","family":"Chang","sequence":"additional","affiliation":[{"name":"College of Biomedicine and Health, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin","family":"Deng","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Wuhan University , Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Wuhan University , Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leng","family":"Han","sequence":"additional","affiliation":[{"name":"Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University , Houston, TX, 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunhua","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Key Laboratory of Traditional Chinese Medicine Toxicology in Forensic Medicine, Guizhou Education Department , Guiyang 550025, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4868-331X","authenticated-orcid":false,"given":"Chunjiang","family":"He","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Wuhan University , Wuhan 430071, China"},{"name":"College of Biomedicine and Health, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,6,1]]},"reference":[{"key":"2022121421224959100_ref1","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/s12943-017-0663-2","article-title":"CircRNA: functions and properties of a novel potential biomarker for cancer","volume":"16","author":"Meng","year":"2017","journal-title":"Mol Cancer"},{"key":"2022121421224959100_ref2","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nature11928","article-title":"Circular RNAs are a large class of animal RNAs with regulatory potency","volume":"495","author":"Memczak","year":"2013","journal-title":"Nature"},{"key":"2022121421224959100_ref3","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/nature11993","article-title":"Natural RNA circles function as efficient microRNA sponges","volume":"495","author":"Hansen","year":"2013","journal-title":"Nature"},{"key":"2022121421224959100_ref4","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/s12943-020-01246-x","article-title":"CircRNA inhibits DNA damage repair by interacting with host gene","volume":"19","author":"Xu","year":"2020","journal-title":"Mol Cancer"},{"key":"2022121421224959100_ref5","doi-asserted-by":"crossref","first-page":"3918","DOI":"10.1158\/1078-0432.CCR-16-2541","article-title":"Circular RNA ciRS-7-A promising prognostic biomarker and a potential therapeutic target in colorectal cancer","volume":"23","author":"Wing","year":"2017","journal-title":"Clin Cancer Res"},{"key":"2022121421224959100_ref6","first-page":"1402","article-title":"Foxo3 circular RNA promotes cardiac senescence by modulating multiple factors associated with stress and senescence responses","volume":"38","author":"Du","year":"2017","journal-title":"Eur Heart J"},{"key":"2022121421224959100_ref7","doi-asserted-by":"crossref","first-page":"2138","DOI":"10.1158\/0008-5472.CAN-19-3268","article-title":"CircFOXK2 promotes growth and metastasis of pancreatic ductal adenocarcinoma by complexing with RNA-binding proteins and sponging MiR-942","volume":"80","author":"Wong","year":"2020","journal-title":"Cancer Res"},{"key":"2022121421224959100_ref8","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/cr.2017.31","article-title":"Extensive translation of circular RNAs driven by N(6)methyladenosine","volume":"27","author":"Yang","year":"2017","journal-title":"Cell 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