RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Over 100 RNA modifications exist, but their positions and functions remain largely unknown.
• High-throughput sequencing methods are emerging to identify RNA modifications.
• Understanding RNA modification landscapes is crucial for deciphering gene regulation.

Purpose of the Study:

• To develop RMBase, a novel database resource for RNA modifications.
• To decode the genome-wide landscape of RNA modifications using existing high-throughput data.
• To provide a centralized platform for exploring RNA modification data and their functional implications.

Main Methods:

• Integrated high-throughput modification sequencing data from 18 independent studies.
• Collected and curated data for pseudouridine (Ψ), 5-methylcytosine (m(5)C), N6-methyladenosine (m(6)A), and 2'-O-methylations (2'-O-Me).
• Developed web interfaces, a genome browser, and a modTool for data querying, annotation, and visualization.

Main Results:

• RMBase release includes ~9,500 Ψ, ~1,000 m(5)C, ~124,200 m(6)A, and ~1,210 2'-O-Me modifications.
• The database integrates diverse experimentally supported RNA modifications.
• RMBase links modification sites with microRNA targets and disease-related SNPs.

Conclusions:

• RMBase provides a comprehensive genome-wide view of RNA modifications.
• The database facilitates the exploration of RNA modification functions and their roles in biological processes.
• RMBase is a valuable resource for researchers studying RNA modifications and their impact on gene expression and disease.