N⁶-methyladenosine (m⁶A) is currently the most prevalent RNA modification on mRNAs and lncRNAs, and plays a pivotal role during various biological processes and disease pathogenesis. Here, we developed m⁶A-Atlas, a comprehensive knowledgebase for unraveling the m⁶A epitranscriptome. (1) 442162 high-confidence m⁶A sites identified from seven base-resolution technologies were collected, and the quantitative (rather than binary) epitranscriptome profiles were estimated from 1363 high-throughput sequencing samples. (2) The conservation of m⁶A sites among seven vertebrate species, including human, mouse and chimp, and the 10 viruses’ m⁶A epitranscriptomes, including HIV, KSHV and DENV. (3) The putative biological functions of individual m⁶A sites predicted from epitranscriptome data, and the potential pathogenesis of m⁶A sites inferred from disease-associated genetic mutations that can directly destroy m⁶A directing sequence motifs. (4) Annotation of m⁶A epitranscriptome sites with post-transcriptional machinery (RBP-binding, microRNA interaction and splicing sites), and the landscape of multiple RNA modifications, together provided users to browse and do further studies.

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