ArticleNucleic acids research2023
G-quadruplex DNA contributes to RNA polymerase II-mediated 3D chromatin architecture.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 49 citations in OpenAlex.
- G-quadruplex structures as regulators of cellular processes and drivers of genome instability in cancer.Critical reviews in biochemistry and molecular biology · 2026Review
- Transposon targeting non-coding RNA transcription targets G/C-rich tracts and is facilitated by an intrinsically disordered protein in Tetrahymena.Science China. Life sciences · 2026Article
- The G-force in the genome: Unknowns on the functional flairs of DNA G-quadruplexes.PLoS biology · 2026Article
- Variation and selection at predicted G-quadruplexes across the human pangenome.bioRxiv : the preprint server for biology · 2026Article
- Metabolic disease variants rewire gene regulation through disruption of DNA G-quadruplex structures.Genome biology · 2026Article
- Photoclick chemistry led to the identification of HELLS as a helicase for DNA G-quadruplexes.Nucleic acids research · 2026Article
- Stability of non-canonical nucleic acid structure as a potential modulator of cell fate.Nucleic acids research · 2026Review
- Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes.bioRxiv : the preprint server for biology · 2025Article
- Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life.Genome research · 2025Article
- GQ-DNABERT reveals GQ proximal enhancer-promoter interactions associated with tissue-specific transcription.Nucleic acids research · 2025Article
- The emerging sequence grammar of 3D genome organisation.Human genetics · 2025Review
- DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights.Genome biology · 2025Article
- G-quadruplexes as potential traps for superenhancer marker BRD4: ligand-sensitive binding and co-separation in vitro.Nucleic acids research · 2025Article
- The Relevance of G-Quadruplexes in Gene Promoters and the First Introns Associated with Transcriptional Regulation in Breast Cancer.International journal of molecular sciences · 2025Article
- G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer cells.Genome biology · 2025Article
- Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry.bioRxiv : the preprint server for biology · 2025Article
- Genome-Wide Detection of Leukemia Biomarkers from lincRNA-Protein-Coding Gene Interaction Networks in the Three-Dimensional Chromatin Structure.Current issues in molecular biology · 2025Article
- G-Quadruplexes in Tumor Immune Regulation: Molecular Mechanisms and Therapeutic Prospects in Gastrointestinal Cancers.Biomedicines · 2025Review
- Cell redistribution of G quadruplex-structured DNA is associated with morphological changes of nuclei and nucleoli in neurons during tau pathology progression.Brain pathology (Zurich, Switzerland) · 2025Article
- Pervasive RNA-binding protein enrichment on TAD boundaries regulates TAD organization.Nucleic acids research · 2025Article
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3 authors at 1 institution in 1 country.
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Abstract
High-order chromatin organization plays an important role in biological processes and disease development. Previous studies revealed a widespread occurrence of guanine quadruplex (G4) structures in the human genome, with enrichment in gene regulatory regions, especially in promoters. However, it remains unclear whether G4 structures contribute to RNA polymerase II (RNAPII)-mediated long-range DNA interactions and transcription activity. In this study, we conducted an intuitive overlapping analysis of previously published RNAPII ChIA-PET (chromatin interaction analysis with paired-end tag) and BG4 ChIP-seq (chromatin immunoprecipitation followed by sequencing using a G4 structure-specific antibody) data. We observed a strong positive correlation between RNAPII-linked DNA loops and G4 structures in chromatin. Additionally, our RNAPII HiChIP-seq (in situ Hi-C followed by ChIP-seq) results showed that treatment of HepG2 cells with pyridostatin (PDS), a small-molecule G4-binding ligand, could diminish RNAPII-linked long-range DNA contacts, with more pronounced diminutions being observed for those contacts involving G4 structure loci. RNA sequencing data revealed that PDS treatment modulates the expression of not only genes with G4 structures in their promoters, but also those with promoters being connected with distal G4s through RNAPII-linked long-range DNA interactions. Together, our data substantiate the function of DNA G4s in RNAPII-associated DNA looping and transcription regulation.
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