ArticleGenome research2015
GC skew defines distinct RNA polymerase pause sites in CpG island promoters.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation.bioRxiv : the preprint server for biology · 2026Article
- Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo.Developmental cell · 2026Article
- Guanine quadruplexes mediate mitochondrial RNA polymerase pausing.BMC biology · 2025Article
- Nucleolar Pol II interactome reveals TBPL1, PAF1, and Pol I at intergenic rDNA drive rRNA biogenesis.Nature communications · 2024Article
- DAXX promotes centromeric stability independently of ATRX by preventing the accumulation of R-loop-induced DNA double-stranded breaks.Nucleic acids research · 2024Article
- U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes.Molecular cell · 2023Article
- Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures.Nucleic acids research · 2023Article
- High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation.Genome biology · 2022Review
- Conserved DNA sequence features underlie pervasive RNA polymerase pausing.Nucleic acids research · 2021Article
- A dual role for H2A.Z.1 in modulating the dynamics of RNA polymerase II initiation and elongation.Nature structural & molecular biology · 2021Article
- Conserved dual-mode gene regulation programs in higher eukaryotes.Nucleic acids research · 2021Article
- The genomic landscape of 8-oxodG reveals enrichment at specific inherently fragile promoters.Nucleic acids research · 2020Article
- Pausing sites of RNA polymerase II on actively transcribed genes are enriched in DNA double-stranded breaks.The Journal of biological chemistry · 2020Article
- Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation.Genes & development · 2019Review
- Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human.Genome biology · 2018Article
- Born to run: control of transcription elongation by RNA polymerase II.Nature reviews. Molecular cell biology · 2018Review
- Targeting the Polyadenylation Signal of Pre-mRNA: A New Gene Silencing Approach for Facioscapulohumeral Dystrophy.International journal of molecular sciences · 2018Review
- Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP.Molecular cell · 2018Article
- Egr-1 and RNA POL II facilitate glioma cell GDNF transcription induced by histone hyperacetylation in promoter II.Oncotarget · 2017Article
- Orphan CpG islands define a novel class of highly active enhancers.Epigenetics · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
CpG islands (CGIs) are associated with over half of human gene promoters and are characterized by a unique chromatin environment and high levels of bidirectional transcriptional activity relative to surrounding genomic regions, suggesting that RNA polymerase (Pol II) progression past the CGI boundaries is restricted. Here we describe a novel transcriptional regulatory step wherein Pol II encounters an additional barrier to elongation distinct from the promoter-proximal pause and occurring at the downstream boundary of the CGI domain. For most CGI-associated promoters, Pol II exhibits a dominant pause at either the promoter-proximal or this distal site that correlates, both in position and in intensity, with local regions of high GC skew, a sequence feature known to form unique secondary structures. Upon signal-induced gene activation, long-range enhancer contacts at the dominant pause site are selectively enhanced, suggesting a new role for enhancers at the downstream pause. These data point to an additional level of control over transcriptional output at a subset of CGI-associated genes that is linked to DNA sequence and the integrity of the CGI domain.
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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.