StructRMDB: A database of RNA modification sites that affect RNA secondary structure

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Post-transcriptional RNA modifications are crucial for biological processes, affecting RNA structure and function.
• Advancements in prediction algorithms enable RNA secondary structure prediction for modified RNA sequences.

Purpose of the Study:

• Introduce StructRMDB, the first database to characterize the impact of chemical modifications on RNA secondary structure.
• Provide a comprehensive resource for studying RNA modification effects on structure.

Main Methods:

• Compiled over 880,000 RNA modification sites and their structural impacts from nine species.
• Utilized RNAstructure and ViennaRNA tools with four scoring methods to assess structural changes.
• Visualized RNA secondary structures with and without modifications to highlight alterations.

Main Results:

• StructRMDB includes data on N6-Methyladenosine (m6A), pseudouridine (Ψ), and adenosine-to-inosine editing (A-to-I) in pre- and mature RNA.
• Quantified structural impacts using Similarity Score, Relative Score, Distance, and SMC Score.
• Demonstrated significant structural alterations induced by RNA modifications.

Conclusions:

• StructRMDB offers novel insights into the effects of RNA modifications on secondary structure.
• Serves as a valuable resource for researchers studying RNA structure and function.
• Provides a user-friendly interface for accessing, downloading, and sharing modification data.