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Published on: May 14, 2020
RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications
Jiajia Xuan1,2, Lifan Chen1, Zhirong Chen1
1MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
RMBase v3.0 is a comprehensive platform for studying RNA modifications, offering tools to explore their landscape, biogenesis, and functions across species. It maps 73 RNA modifications and aids in understanding their roles in various biological processes and diseases.
Area of Science:
- * Molecular Biology
- * Bioinformatics
- * Genomics
Background:
- * Over 170 chemical RNA modifications are known, but their prevalence, mechanisms, and functions are largely uncharacterized.
- * Integrated analysis of diverse RNA modification profiles is crucial for understanding epitranscriptomics.
- * Existing resources lack comprehensive tools for exploring RNA modification data.
Purpose of the Study:
- * To develop RMBase v3.0, an integrated platform with eight modules for analyzing RNA modifications.
- * To provide a comprehensive resource for exploring the transcriptome-wide landscape, biogenesis, interactome, and functions of RNA modifications.
- * To facilitate the study of RNA modification patterns, mechanisms, and their relationship with other biological factors.
Main Methods:
- * Development of RMBase v3.0, a web-based platform with eight specialized modules.
- * Mining of thousands of epitranscriptome datasets using novel bioinformatics pipelines.
- * Integration of data on RNA modifications, genes, enzymes, histone modifications, RNA-modifying proteins (RMPs), RBPs, miRNAs, and SNPs.
Main Results:
- * RMBase v3.0 maps 73 RNA modifications across 62 species, detailing their transcriptome-wide distribution.
- * The platform elucidates biogenesis mechanisms for 23,382 modified sites and explores correlations with histone modifications.
- * It investigates differential expression of 146 RMPs in 18 cancer types and integrates interactional relationships with various molecular factors.
Conclusions:
- * RMBase v3.0 serves as a valuable, comprehensive resource for the epitranscriptomics community.
- * The platform offers diverse tools and integrated data for in-depth study of RNA modifications.
- * RMBase v3.0 facilitates research into the roles of RNA modifications in gene regulation and disease.
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