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EndoQuad: a comprehensive genome-wide experimentally validated endogenous G-quadruplex database.

Sheng Hu Qian1, Meng-Wei Shi1, Yu-Li Xiong1

  • 1Hubei Hongshan Laboratory, College of Life Science and Technology, College of Biomedicine and Health, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, PR China.

Nucleic Acids Research
|October 31, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces EndoQuad, a database of endogenous G-quadruplexes (eG4s) identified through high-throughput experiments. EndoQuad provides a comprehensive resource for exploring eG4s and their regulatory roles in genetics and disease.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • G-quadruplexes (G4s) are non-canonical DNA structures with emerging roles in genetic regulation.
  • Comprehensive genomic annotation and characterization of endogenous G4s (eG4s) and their regulatory networks are currently lacking.
  • Existing gaps hinder in-depth research into eG4s and their functional significance.

Purpose of the Study:

  • To develop EndoQuad, a comprehensive and interactive database of experimentally validated endogenous DNA G-quadruplexes (eG4s).
  • To integrate high-throughput experimental data for genome-wide eG4 mapping and characterization.
  • To facilitate research on eG4s by providing a centralized resource for accessing, downloading, and repurposing data.

Main Methods:

  • Generation of genome-wide eG4s mapping datasets using G4 ChIP-seq/CUT&Tag in human, mouse, and chicken.
  • Multi-omics analyses to characterize eG4s, including cell-type specificity, structural stability, evolutionary conservation, and genomic enrichment.
  • Integration of functional genomic variants to prioritize eG4s with regulatory roles in disease and cancer.

Main Results:

  • A reference set of genome-wide eG4s was generated, with most identified in specific cell types.
  • eG4s with higher occurrence across samples exhibited greater structural stability, evolutionary conservation, and enrichment in promoter regions.
  • These high-confidence eG4s were associated with highly expressed genes and complex regulatory programs, including roles in disease and cancer.

Conclusions:

  • EndoQuad serves as a valuable, one-stop resource for eG4 research, consolidating experimentally validated data.
  • The database enables users to access and utilize eG4 data for diverse research applications.
  • EndoQuad lays the foundation for future functional studies on G-quadruplexes and their regulatory impact.