RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for...

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• RNA structure is vital for biological functions and RNA-targeted therapies.
• Limited validated RNA structural targets hinder drug design.

Purpose of the Study:

• To create the first genome-scale map of the human RNA structurome.
• To identify stable RNA structures for therapeutic targeting.
• To develop an integrated pipeline for RNA structure-function analysis.

Main Methods:

• Applied ScanFold to over 230,000 human pre-mRNA transcripts.
• Performed global analysis of low-z-score regions and their 2D folding patterns.
• Developed the RNA-Annotator Pipeline integrating structural data with 20 biological annotations.

Main Results:

• Generated a genome-scale map of the human RNA structurome, identifying sequences with stable secondary structures.
• Characterized folding patterns and identified high-confidence RNA structures.
• Demonstrated the pipeline's utility by analyzing SMN1/SMN2 pre-mRNAs, revealing structural changes affecting splicing.

Conclusions:

• The RNA structurome map provides insights for prioritizing RNA targets in drug discovery.
• The RNA-Annotator Pipeline facilitates exploration of RNA structure-function relationships.
• This work accelerates advances in RNA-targeted drug discovery and RNA biology research.