Variation and selection at predicted G-quadruplexes across the human pangenome.

Area of Science:

• Genomics
• Molecular Biology
• Human Genetics

Background:

• G-quadruplexes (G4s) are non-canonical DNA structures with significant roles in cellular functions like transcription and replication.
• G4 motifs are implicated in genomic instability, mutations, and structural variations.
• Detailed analysis of G4 motifs across diverse human genomes is lacking.

Purpose of the Study:

• To comprehensively analyze the presence, absence, and sequence variation of predicted G4s (pG4s) across human populations.
• To measure selection strength and evaluate the gene expression regulation potential of pG4s.
• To understand the functional relevance of G4s in both coding and regulatory genomic regions.

Main Methods:

• Utilized the Human Pangenome Reference Consortium dataset (231 individuals) for high-quality diploid genome analysis.
• Identified over 353 million pG4s, including novel ones absent from reference assemblies.
• Analyzed site frequency spectrum to compute selection coefficients (Sd) at pG4 versus non-pG4 sites.
• Integrated pG4 data with long-read transcriptome data to assess gene expression regulation.

Main Results:

• pG4 sharing patterns reflect human population structure, with lower sharing in African and higher sharing in East Asian individuals.
• pG4 sites in regulatory regions (promoters, introns, enhancers) exhibit stronger purifying selection than non-pG4 sites.
• pG4s at promoters and exon-intron junctions influence gene expression variation and transcript isoform diversity.

Conclusions:

• G-quadruplexes are functionally relevant across the human pangenome, particularly in regulatory regions.
• pG4s contribute to gene expression regulation and transcript variation, highlighting their importance beyond coding sequences.
• This large-scale population analysis provides fundamental insights into the significance and functional roles of G4s in the human genome.