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

Bowen SONG; Daiyun HUANG; Yuxin ZHANG; Zhen WEI; Jionglong SU; João PEDRO DE MAGALHÃES; Daniel J RIGDEN; Jia MENG; Kunqi CHEN

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m6A-TSHub: Unveiling the Context-specific m⁶A Methylation and m⁶A-affecting Mutations in 23 Human Tissues.

Author: Bowen SONG ¹ ; Daiyun HUANG ² ; Yuxin ZHANG ³ ; Zhen WEI ⁴ ; Jionglong SU ⁵ ; João PEDRO DE MAGALHÃES ⁶ ; Daniel J RIGDEN ⁷ ; Jia MENG ⁸ ; Kunqi CHEN ⁹
Author Information

1. Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China; Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.
2. Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Department of Computer Science, University of Liverpool, Liverpool L69 7ZB, United Kingdom. Electronic address: daiyun.huang@liverpool.ac.uk.
3. Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China.
4. Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Ageing & Chronic Disease, University of Liverpool, Liverpool L69 7ZB, United Kingdom.
5. School of AI and Advanced Computing, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China.
6. Institute of Ageing & Chronic Disease, University of Liverpool, Liverpool L69 7ZB, United Kingdom.
7. Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.
8. Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China.
9. Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China. Electronic address: kunqi.chen@fjmu.edu.cn.
Publication Type:Journal Article
Keywords: Cancer mutation; Context-specific analysis; Functional annotation; Genome analysis; N(6)-methyladenosine
MeSH: Humans; Methylation; RNA, Messenger/metabolism*; Neoplasms/genetics*; Mutation
From: Genomics, Proteomics & Bioinformatics 2023;21(4):678-694
CountryChina
Language:English
Abstract: As the most pervasive epigenetic marker present on mRNAs and long non-coding RNAs (lncRNAs), N⁶-methyladenosine (m⁶A) RNA methylation has been shown to participate in essential biological processes. Recent studies have revealed the distinct patterns of m⁶A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m⁶A methylation. We present here a comprehensive online platform, m6A-TSHub, for unveiling the context-specific m⁶A methylation and genetic mutations that potentially regulate m⁶A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB, a comprehensive database of 184,554 functionally annotated m⁶A sites derived from 23 human tissues and 499,369 m⁶A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder, a web server for high-accuracy prediction of m⁶A 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 m⁶A 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 m⁶A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m⁶A 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.

m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues.

m6A-TSHub: Unveiling the Context-specific m⁶A Methylation and m⁶A-affecting Mutations in 23 Human Tissues.