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m6Aexpress-Reader : Prediction of m 6 A regulated expression genes by integrating m 6 A sites and reader binding information in specific- context

Methods, ISSN: 1046-2023, Vol: 203, Page: 167-178
2022
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Article Description

N 6 -methyladenosine (m 6 A) is the most abundant form of mRNA modification and plays an important role in regulating gene expression. However, the mechanisms of m 6 A regulated gene expression in cell or condition specific, are still poorly understood. Even though, some methods are able to predict m 6 A regulated expression (m 6 A-reg-exp) genes in specific context, they don’t introduce the m 6 A reader binding information, while this information can help to predict m 6 A-reg-exp genes and more clearly to explain the mechanisms of m 6 A-mediated gene expression process. Thus, by integrating m 6 A sites and reader binding information, we proposed a novel method (called m6Aexpress-Reader ) to predict m 6 A-reg-exp genes from limited MeRIP-seq data in specific context. m6Aexpress-Reader adopts the reader binding signal strength to weight the posterior distribution of the estimated regulatory coefficients for enhancing the prediction power. By using m6Aexpress-Reader, we found the complex characteristic of m 6 A on gene expression regulation and the distinct regulated pattern of m 6 A-reg-exp genes with different reader binding. m 6 A readers, YTHDF2 or IGF2BP1/3 all play an important role in various cancers and the key cancer pathways. In addition, m6Aexpress-Reader reveals the distinct m 6 A regulated mode of reader targeted genes in cancer. m6Aexpress-Reader could be a useful tool for studying the m 6 A regulation on reader target genes in specific context and it can be freely accessible at: https://github.com/NWPU-903PR/m6AexpressReader.

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