RNAmod – an integrated system for the annotation of mRNA modifications

Dynamic and reversible RNA modifications such as N6-methyladenosine (m6A) can play important roles in regulating messenger RNA (mRNA) splicing, export, stability and translation. Defective mRNA modification through altered expression of the methyltransferase and/or demethylases results in developmental defects and cancer progression. Identifying modified mRNAs, annotating the distribution of modification sites across the mRNA, as well as characterizing and comparing other modification features are essential for studying the function and elucidating the mechanism of mRNA modifications. Several methods including methylated RNA immunoprecipitation and sequencing (MeRIP-seq) are available for the detection of mRNA modifications. However, a convenient and comprehensive tool to annotate diverse kinds of mRNA modifications in different species is lacking.

Researchers at Boston Children’s Hospital, and Harvard Medical School, have developed RNAmod, an interactive, one-stop, web-based platform for the automated analysis, annotation, and visualization of mRNA modifications in 21 species. RNAmod provides intuitive interfaces to show outputs including the distribution of RNA modifications, modification coverage for different gene features, functional annotation of modified mRNAs, and comparisons between different groups or specific gene sets. Furthermore, sites of known RNA modification, as well as binding site data for hundreds of RNA-binding proteins (RBPs) are integrated in RNAmod to help users compare their modification data with known modifications and to explore the relationship with the binding sites of known RBPs. RNAmod is freely available and meets the emerging need for a convenient and comprehensive analysis tool for the fast-developing RNA modification field.

Overall workflow of RNAmod

rna-seq

RNAmod provides three functional modules, including single case, group case, and gene case. The single case module allows users to annotate RNA modifications for a single sample. The group case module allows users to annotate and compare the modification distribution between two samples or even more groups. The gene case analysis module can be used to analyze the modification distribution in the context of specific genes.

Availabilityhttps://bioinformatics.sc.cn/RNAmod

Liu Q, Gregory RI. (2019) RNAmod: an integrated system for the annotation of mRNA modifications. Nucleic Acids Res [Epub ahead of print]. [article]

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