AStruct

AStruct detects allele-specific RNA secondary structures from RT-stop based structuromic probing data to identify functional genetic variants that alter RNA structure.

Key Features:

• Allele-Specific Detection: Detects allele-specific RNA secondary structures (ASRS) at heterozygous single nucleotide polymorphisms (SNPs) to reveal variant-dependent structural differences.
• RT-stop Structuromics: Leverages RT-stop based structuromic probing data to capture RNA secondary structure signatures under cellular conditions.
• Data Integration: Integrates allelic variant information, base-pairing interactions, and RT-stop signals for combined analysis of structure and sequence variation.
• Performance and Validation: Demonstrated robust performance on simulated datasets and public icSHAPE datasets.
• Functional Insights: Higher-scoring SNPs are enriched in coding regions and frequently disrupt m6A modification sites or protein-binding sites and associate with disease.
• Dynamic Analysis: Considers dynamic cellular conditions when detecting functional allele-specific structural changes.

Scientific Applications:

• Gene Regulation Studies: Identify how genetic variants influence RNA structure and thereby affect gene expression and regulation.
• Genetic Disease Research: Pinpoint SNPs whose allele-specific structural effects associate with disease and potential functional impact.
• RNA Biology: Elucidate roles of RNA secondary structure in processes such as m6A modification, protein binding, translation, and splicing.

Methodology:

Integrates allelic variants, base-pairing interactions, and RT-stop based structuromic probing data and analyzes these signals to detect allele-specific RNA secondary structures at heterozygous SNPs across cellular conditions.