m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.

Ma, Jiongming, Song, Bowen, Wei, Zhen, Huang, Daiyun, Zhang, Yuxin, Su, Jionglong, de Magalhães, João Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Meng, Jia ORCID: 0000-0003-3455-205X and Chen, Kunqi
(2022) m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome. Nucleic acids research, 50 (D1). D196-D203.

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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.

Item Type: Article
Uncontrolled Keywords: Humans, 5-Methylcytosine, MicroRNAs, Sequence Analysis, RNA, RNA Processing, Post-Transcriptional, Polymorphism, Single Nucleotide, Software, Databases, Genetic, Transcriptome, Epigenome
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Faculty of Science and Engineering > School of Electrical Engineering, Electronics and Computer Science
Depositing User: Symplectic Admin
Date Deposited: 31 Jan 2022 09:14
Last Modified: 27 Nov 2023 02:24
DOI: 10.1093/nar/gkab1075
Open Access URL: https://academic.oup.com/nar/article/50/D1/D196/64...
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URI: https://livrepository.liverpool.ac.uk/id/eprint/3147828