TY - JOUR
T1 - M5C-Atlas
T2 - A comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome
AU - Ma, Jiongming
AU - Song, Bowen
AU - Wei, Zhen
AU - Huang, Daiyun
AU - Zhang, Yuxin
AU - Su, Jionglong
AU - De Magalhães, João Pedro
AU - Rigden, Daniel J.
AU - Meng, Jia
AU - Chen, Kunqi
N1 - 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.
PY - 2022/1/7
Y1 - 2022/1/7
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85123231439&partnerID=8YFLogxK
U2 - 10.1093/nar/gkab1075
DO - 10.1093/nar/gkab1075
M3 - Article
C2 - 34986603
AN - SCOPUS:85123231439
SN - 0305-1048
VL - 50
SP - D196-D203
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -