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bioRxiv · 10.1101/2022.01.12.476117

m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues

Song, B.·Huang, D.·Zhang, Y.·Wei, Z.·Su, J.·Magalhaes, J. P. d.·Rigden, D.·Meng, J.·Chen, K.
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Abstract

As the most pervasive epigenetic marker present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies 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 modification; and (4) m6A-CAVar: a database of 587,983 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 genetic factor of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at: www.xjtlu.edu.cn/biologicalsciences/m6ats.

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Song, B., Huang, D., Zhang, Y., Wei, Z., Su, J., Magalhaes, J. P. d., Rigden, D., Meng, J., Chen, K.. 2022-01-14. m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues. https://doi.org/10.1101/2022.01.12.476117

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