EndoQuad

EndoQuad provides a curated, experimentally validated database of endogenous G-quadruplexes (eG4s), non-canonical four‑stranded DNA structures, and integrates G4 ChIP-seq and CUT&Tag-derived genome-wide mappings with multi-omics and functional variant data to support analysis of eG4 roles in gene regulation and disease.

Key Features:

• Experimentally validated reference set: Genome-wide catalogue of experimentally validated eG4s including human (1,181 identified), mouse (24), and chicken (2).
• High-throughput data sources: eG4 mappings derived from G4 ChIP-seq and CUT&Tag experiments.
• Multi-omics analyses: Integrates multi-omics data to characterize eG4s across molecular contexts.
• Cell-type specificity: Analysis shows most eG4s are cell-type specific across samples.
• Stability and conservation: eG4s observed across multiple samples display greater structural stability and evolutionary conservation.
• Genomic distribution: eG4s are enriched in promoter regions and are associated with highly expressed genes.
• Regulatory association: eG4s are linked to complex regulatory programs implicating roles in gene regulation.
• Variant integration and prioritization: Integration of millions of functional genomic variants enables prioritization of eG4s with potential regulatory roles in disease and cancer contexts.

Scientific Applications:

• Gene regulation analysis: Characterizing the contribution of eG4s to promoter activity and expression of highly expressed genes.
• Disease and cancer prioritization: Prioritizing eG4s that overlap functional genomic variants implicated in disease and cancer.
• Cell-type and context-specific studies: Studying cell-type specific eG4 landscapes and their regulatory consequences.
• Evolutionary and structural studies: Investigating structural stability and evolutionary conservation of recurrent eG4s across species.
• Target selection for functional experiments: Informing selection of experimentally tractable eG4 loci for downstream functional studies.

Methodology:

Integrates high-throughput G4 ChIP-seq and CUT&Tag data to build a genome-wide reference of experimentally validated eG4s, performs multi-omics analyses, and maps millions of functional genomic variants to eG4 loci.