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RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data.
Jia-Jia Xuan1,2, Wen-Ju Sun1,2, Peng-Hui Lin1,2
1Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, PR China.
Nucleic Acids Research
|October 18, 2017
Summary
RMBase v2.0 is a comprehensive database detailing RNA modifications across 13 species. It integrates epitranscriptome data to explore RNA modification functions and relationships with miRNAs, SNPs, and RNA-binding proteins.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Over 100 RNA modifications exist, but their prevalence, mechanisms, and functions are largely unknown.
- Understanding these modifications is crucial for deciphering gene regulation and cellular processes.
Purpose of the Study:
- To develop RMBase v2.0, a comprehensive database for transcriptome-wide RNA modification landscapes.
- To integrate epitranscriptome sequencing data for exploring RNA modifications and their associations with biological factors.
Main Methods:
- RMBase v2.0 integrates approximately 600 datasets and 1,397,000 modification sites from 47 studies across 13 species.
- The database includes data on N6-methyladenosine (m6A), N1-methyladenosine (m1A), pseudouridine (Ψ), 5-methylcytosine (m5C), and 2'-O-methylations (2'-O-Me).
- New modules for analyzing modification motifs (Motif), RNA modification-RBP interactions (modRBP), and modification patterns along transcripts (modMetagene) were developed.
Main Results:
- RMBase v2.0 represents a tenfold expansion compared to its previous release, offering extensive epitranscriptomic data.
- The database provides detailed information on millions of RNA modification sites, including specific types like m6A and Ψ.
- Novel tools facilitate visualization of modification motifs, exploration of RBP associations, and analysis of modification patterns across transcript models.
Conclusions:
- RMBase v2.0 serves as a valuable resource for researchers studying RNA modifications.
- The database aids in investigating the potential functions and mechanisms of diverse RNA modifications.
- RMBase v2.0 facilitates deeper understanding of epitranscriptomics and its role in biological processes.