ArticleNucleic acids research2013
Bioinformatic analysis reveals an evolutional selection for DNA:RNA hybrid G-quadruplex structures as putative transcription regulatory elements in warm-blooded animals.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 71 citations in OpenAlex.
- The stability and unfolding of DNA: RNA hybrid G-quadruplexes.Nucleic acids research · 2025Article
- Review
- DNA supercoiling-mediated G4/R-loop formation tunes transcription by controlling the access of RNA polymerase.Nature communications · 2025Article
- Protocol for forming G-quadruplexes from double-stranded DNA during transcription.STAR protocols · 2025Article
- Dominant and genome-wide formation of DNA:RNA hybrid G-quadruplexes in living yeast cells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity.Nucleic acids research · 2024Article
- Single-molecule observation of G-quadruplex and R-loop formation induced by transcription.Methods in enzymology · 2024Article
- Alternative splicing modulation by G-quadruplexes.Nature communications · 2022Article
- G-quadruplex structural variations in human genome associated with single-nucleotide variations and their impact on gene activity.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution.Communications biology · 2021Article
- Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back.Nucleic acids research · 2020Article
- Detection of genomic G-quadruplexes in living cells using a small artificial protein.Nucleic acids research · 2020Article
- Epigenetic Modulation of Chromatin States and Gene Expression by G-Quadruplex Structures.International journal of molecular sciences · 2020Review
- DNA:RNA hybrid G-quadruplex formation upstream of transcription start site.Scientific reports · 2020Article
- Structure and Function of Multimeric G-Quadruplexes.Molecules (Basel, Switzerland) · 2019Review
- Binding of cellular nucleolin with the viral core RNA G-quadruplex structure suppresses HCV replication.Nucleic acids research · 2019Article
- RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms.Journal of molecular biology · 2017Review
- Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery.Biochemistry. Biokhimiia · 2016Article
- Yeast Helicase Pif1 Unwinds RNA:DNA Hybrids with Higher Processivity than DNA:DNA Duplexes.The Journal of biological chemistry · 2016Article
- Guanine-vacancy-bearing G-quadruplexes responsive to guanine derivatives.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently, we reported the co-transcriptional formation of DNA:RNA hybrid G-quadruplex (HQ) structure by the non-template DNA strand and nascent RNA transcript, which in turn modulates transcription under both in vitro and in vivo conditions. Here we present bioinformatic analysis on putative HQ-forming sequences (PHQS) in the genomes of eukaryotic organisms. Starting from amphibian, PHQS motifs are concentrated in the immediate 1000-nt region downstream of transcription start sites, implying their potential role in transcription regulation. Moreover, their occurrence shows a strong bias toward the non-template versus the template strand. PHQS has become constitutional in genes in warm-blooded animals, and the magnitude of the strand bias correlates with the ability of PHQS to form HQ, suggesting a selection based on HQ formation. This strand bias is reversed in lower species, implying that the selection of PHQS/HQ depended on the living temperature of the organisms. In comparison with the putative intramolecular G-quadruplex-forming sequences (PQS), PHQS motifs are far more prevalent and abundant in the transcribed regions, making them the dominant candidates in the formation of G-quadruplexes in transcription. Collectively, these results suggest that the HQ structures are evolutionally selected to function in transcription and other transcription-mediated processes that involve guanine-rich non-template strand.
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