ArticleNucleic acids research2015
GC skew is a conserved property of unmethylated CpG island promoters across vertebrates.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 65 citations in OpenAlex.
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- Genome biology of long non-coding RNAs in humans: A virtual karyotype.Computational and structural biotechnology journal · 2025Article
- Beyond the "Dominant" and "Recessive" Patterns of Inheritance.International journal of molecular sciences · 2024Article
- RNA biogenesis and RNA metabolism factors as R-loop suppressors: a hidden role in genome integrity.Genes & development · 2024Review
- Covalent PARylation of DNA base excision repair proteins regulates DNA demethylation.Nature communications · 2024Article
- p53-dependent R-loop formation and HPV pathogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Targeting of the Interleukin-13 Receptor (IL-13R)α2 Expressing Prostate Cancer by a Novel Hybrid Lytic Peptide.Biomolecules · 2023Article
- Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria.Microbial genomics · 2022Article
- Article
- Genomic patterns of transcription-replication interactions in mouse primary B cells.Nucleic acids research · 2022Article
- Review
- Mapping R-Loops and RNA:DNA Hybrids with S9.6-Based Immunoprecipitation Methods.Journal of visualized experiments : JoVE · 2021Article
- A CpG island promoter drives the CXXC5 gene expression.Scientific reports · 2021Article
- A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation.Nucleic acids research · 2021Article
- Best practices for the visualization, mapping, and manipulation of R-loops.The EMBO journal · 2021Review
- G-quadruplex-R-loop interactions and the mechanism of anticancer G-quadruplex binders.Nucleic acids research · 2020Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
GC skew is a measure of the strand asymmetry in the distribution of guanines and cytosines. GC skew favors R-loops, a type of three stranded nucleic acid structures that form upon annealing of an RNA strand to one strand of DNA, creating a persistent RNA:DNA hybrid. Previous studies show that GC skew is prevalent at thousands of human CpG island (CGI) promoters and transcription termination regions, which correspond to hotspots of R-loop formation. Here, we investigated the conservation of GC skew patterns in 60 sequenced chordates genomes. We report that GC skew is a conserved sequence characteristic of the CGI promoter class in vertebrates. Furthermore, we reveal that promoter GC skew peaks at the exon 1/ intron1 junction and that it is highly correlated with gene age and CGI promoter strength. Our data also show that GC skew is predictive of unmethylated CGI promoters in a range of vertebrate species and that it imparts significant DNA hypomethylation for promoters with intermediate CpG densities. Finally, we observed that terminal GC skew is conserved for a subset of vertebrate genes that tend to be located significantly closer to their downstream neighbors, consistent with a role for R-loop formation in transcription termination.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.