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

Jiongming Ma, Bowen Song, Zhen Wei, Daiyun Huang, Yuxin Zhang, Jionglong Su, João Pedro De magalhães, Daniel J Rigden, Jia Meng, Kunqi Chen

Research output: Contribution to journalArticlepeer-review

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Abstract

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.

Original languageEnglish
Pages (from-to)D196-D203
Number of pages8
JournalNucleic Acids Research
Volume50
Issue numberD1
Early online date19 Nov 2021
DOIs
Publication statusPublished - 7 Jan 2022

Bibliographical note

Funding Information:
National Natural Science Foundation of China [31671373]; XJTLU Key Program Special Fund [KSF-T-01, KSF-E-51 and KSF-P-02].

Publisher Copyright:
© 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.

Keywords

  • 5-Methylcytosine/chemistry
  • Databases, Genetic
  • Epigenome/genetics
  • Humans
  • MicroRNAs/genetics
  • Polymorphism, Single Nucleotide/genetics
  • RNA Processing, Post-Transcriptional/genetics
  • Sequence Analysis, RNA
  • Software
  • Transcriptome/genetics

ASJC Scopus subject areas

  • Genetics

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