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

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