G4SNVHunter: An R/Bioconductor Package for Evaluating SNV-Induced Disruption of G-Quadruplex Structures Leveraging...

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• G-quadruplexes (G4s) are crucial nucleic acid structures involved in gene regulation.
• Single-nucleotide variants (SNVs) can alter G4 formation, impacting biological functions.
• A need exists for specialized tools to analyze SNV effects on G4 structures.

Purpose of the Study:

• To introduce G4SNVHunter, an R/Bioconductor package for detecting variants affecting G4 formation.
• To provide a quantitative assessment of G4 propensity changes due to SNVs.
• To facilitate experimental validation of G4 structure disruption by genetic variants.

Main Methods:

• Development of the G4SNVHunter R/Bioconductor package.
• Utilizing the G4Hunter algorithm's principles for G4 propensity assessment.
• Analysis of archaic introgressed variants from Neandertal and Denisovan populations.

Main Results:

• G4SNVHunter enables rapid detection of variants impacting G4 structures.
• Analysis identified ~5,800 variants in G4 regions within archaic introgression data.
• Approximately 230 variants were predicted to impair G4 structure formation propensity.

Conclusions:

• G4SNVHunter is a valuable tool for assessing the impact of genetic variants on G4 structures.
• The findings highlight potential functional consequences of archaic variants on G4-mediated regulation.
• The package facilitates deeper understanding of genetic variation's role in G4 biology.