{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T11:08:34Z","timestamp":1785150514126,"version":"3.55.0"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,19]],"date-time":"2021-11-19T00:00:00Z","timestamp":1637280000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31671373"],"award-info":[{"award-number":["31671373"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"XJTLU Key Program Special Fund","award":["KSF-T-01"],"award-info":[{"award-number":["KSF-T-01"]}]},{"name":"XJTLU Key Program Special Fund","award":["KSF-E-51"],"award-info":[{"award-number":["KSF-E-51"]}]},{"name":"XJTLU Key Program Special Fund","award":["KSF-P-02"],"award-info":[{"award-number":["KSF-P-02"]}]},{"name":"School of Basic Medical Sciences, Fujian Medical University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>5-Methylcytosine (m5C) is one of the most prevalent covalent modifications on RNA. It is known to regulate a broad variety of RNA functions, including nuclear export, RNA stability and translation. Here, we present m5C-Atlas, a database for comprehensive collection and annotation of RNA 5-methylcytosine. The database contains 166 540 m5C sites in 13 species identified from 5 base-resolution epitranscriptome profiling technologies. Moreover, condition-specific methylation levels are quantified from 351 RNA bisulfite sequencing samples gathered from 22 different studies via an integrative pipeline. The database also presents several novel features, such as the evolutionary conservation of a m5C locus, its association with SNPs, and any relevance to RNA secondary structure. All m5C-atlas data are accessible through a user-friendly interface, in which the m5C epitranscriptomes can be freely explored, shared, and annotated with putative post-transcriptional mechanisms (e.g. RBP intermolecular interaction with RNA, microRNA interaction and splicing sites). Together, these resources offer unprecedented opportunities for exploring m5C epitranscriptomes. The m5C-Atlas database is freely accessible at https:\/\/www.xjtlu.edu.cn\/biologicalsciences\/m5c-atlas.<\/jats:p>","DOI":"10.1093\/nar\/gkab1075","type":"journal-article","created":{"date-parts":[[2021,10,22]],"date-time":"2021-10-22T22:48:56Z","timestamp":1634942936000},"page":"D196-D203","source":"Crossref","is-referenced-by-count":104,"title":["m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome"],"prefix":"10.1093","volume":"50","author":[{"given":"Jiongming","family":"Ma","sequence":"first","affiliation":[{"name":"Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou\u00a0350004, China"},{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bowen","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"},{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Wei","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"},{"name":"Institute of Ageing & Chronic Disease, University of Liverpool, L69 7ZB, Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daiyun","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"},{"name":"Department of Computer Science, University of Liverpool, L69 7ZB, Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuxin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jionglong","family":"Su","sequence":"additional","affiliation":[{"name":"School of AI and Advanced Computing, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu\u00a0215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo\u00e3o Pedro","family":"de\u00a0Magalh\u00e3es","sequence":"additional","affiliation":[{"name":"Institute of Ageing & Chronic Disease, University of Liverpool, L69 7ZB, Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel J","family":"Rigden","sequence":"additional","affiliation":[{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3455-205X","authenticated-orcid":false,"given":"Jia","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"},{"name":"AI University Research Centre, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"},{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6025-8957","authenticated-orcid":false,"given":"Kunqi","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou\u00a0350004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,19]]},"reference":[{"key":"2022010507324935100_B1","doi-asserted-by":"crossref","first-page":"D303","DOI":"10.1093\/nar\/gkx1030","article-title":"MODOMICS: a database of RNA modification pathways. 2017 update","volume":"46","author":"Boccaletto","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022010507324935100_B2","doi-asserted-by":"crossref","first-page":"e1639","DOI":"10.1002\/wrna.1639","article-title":"Dynamic transcriptomic m(5) C and its regulatory role in RNA processing","volume":"12","author":"Chen","year":"2021","journal-title":"Wiley Interdiscip. 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