m6A-TSHub: Unveiling the Context-specific m<sup>6</sup>A Methylation and m<sup>6</sup>A-affecting Mutations in 23 Human Tissues.

Song, Bowen ORCID: 0000-0002-8586-0573, Huang, Daiyun ORCID: 0000-0002-3067-7165, Zhang, Yuxin ORCID: 0000-0003-1900-6712, Wei, Zhen, Su, Jionglong ORCID: 0000-0001-5360-6493, Pedro de Magalhães, João, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Meng, Jia ORCID: 0000-0003-3455-205X and Chen, Kunqi ORCID: 0000-0002-6025-8957
(2023) m6A-TSHub: Unveiling the Context-specific m<sup>6</sup>A Methylation and m<sup>6</sup>A-affecting Mutations in 23 Human Tissues. Genomics, proteomics & bioinformatics, 21 (4). pp. 678-694.

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As the most pervasive epigenetic marker present on mRNAs and long non-coding RNAs (lncRNAs), N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) RNA methylation has been shown to participate in essential biological processes. Recent studies have revealed the distinct patterns of m<sup>6</sup>A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m<sup>6</sup>A methylation. We present here a comprehensive online platform, m6A-TSHub, for unveiling the context-specific m<sup>6</sup>A methylation and genetic mutations that potentially regulate m<sup>6</sup>A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB, a comprehensive database of 184,554 functionally annotated m<sup>6</sup>A sites derived from 23 human tissues and 499,369 m<sup>6</sup>A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder, a web server for high-accuracy prediction of m<sup>6</sup>A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar, a web server for assessing the impact of genetic variants on tissue-specific m<sup>6</sup>A RNA modifications; and (4) m6A-CAVar, a database of 587,983 The Cancer Genome Atlas (TCGA) cancer mutations (derived from 27 cancer types) that were predicted to affect m<sup>6</sup>A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m<sup>6</sup>A methylome and the genetic factors of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at www.xjtlu.edu.cn/biologicalsciences/m6ats.

Item Type: Article
Uncontrolled Keywords: Humans, Neoplasms, RNA, Messenger, Methylation, Mutation
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User: Symplectic Admin
Date Deposited: 19 Sep 2022 11:21
Last Modified: 05 Feb 2024 04:55
DOI: 10.1016/j.gpb.2022.09.001
Open Access URL: https://www.sciencedirect.com/science/article/pii/...
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3164896