Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
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Pressing Pause: The pausing of RNA polymerase II (Pol II) near promoters is an important and distinct regulatory step in the process of transcribing DNA into RNA. Although protein factors and DNA elements involved in pausing have been identified, the post-initiation events that lead to pausing are poorly understood. Kwak et al. (p. 950 ) present an approach, termed PRO-seq, for monitoring the position of actively transcribing RNA polymerase with single-nucleotide precision. The approach was used to explore the mechanism of promoter proximal pausing and showed that precise positioning between core promoter elements and the pause site is critical. The findings show how the promoter dictates transcriptional pausing and detects the preferential localization of active transcription complexes within the genome.
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Higher RNA Pol II accumulation has been reported at spliced exons, as compared to skipped exons.
“Moreover, higher RNA Pol II accumulation has been reported at spliced exons, as compared to skipped exons (Kwak et al, 2013; Mayer et al, 2015; Nojima et al, 2015).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Kwak et al, 2013
PRO-seq and NET-seq confirmed a pause at the 3′ splice site in budding yeast and Drosophila, at the 3′ and 5′ splice sites in human cells, and at the 5′ splice site in plants.
“These methods also confirmed the existence of a pause at the 3′ splice site in budding yeast (Harlen et al, 2016) and Drosophila (Kwak et al, 2013), at the 3′ and 5′ splice sites in human cells (Mayer et al, 2015; Nojima et al, 2015) and at the 5′ splice site in plants (Kindgren et al, 2020).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Kwak et al, 2013
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- Authors
- Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T.
- Affiliations
- Cornell University (US)
- Corresponding author
- Core, Leighton J.
- Lis, John T.
- Venue
- Science
- Published
- 2013-02-22
- Volume
- 339
- Issue
- 6122
- Pages
- 950-953
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3974810
- OpenAlex
- W1985567287
- Cited by
- 849
- References
- 28
- Citations by year
- 2026: 55 · 2025: 62 · 2024: 92 · 2023: 53 · 2022: 78 · 2021: 98 · 2020: 68 · 2019: 76 · 2018: 57 · 2017: 48 · 2016: 61 · 2015: 40 · 2014: 40 · 2013: 20
- FWCI
- 24.06
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Human Genome Research Institute (R01HG004845, HG004845)
- National Institute of General Medical Sciences (R01GM025232, R37GM025232, GM-25232)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- RNA polymerase II, transcription initiation, core promoter elements, PRO-seq, exon-intron junctions, polyadenylation sites, nucleosome positioning, insertional mutagenesis, transcriptional regulation
- MeSH terms
- Animals, Drosophila melanogaster, Gene Expression Regulation, Models, Genetic, Nucleosomes, Promoter Regions, Genetic, RNA Polymerase II, Transcription, Genetic, Mutagenesis, Insertional, Genes, Insect, HSP70 Heat-Shock Proteins, Transgenes, Base Pairing, RNA Splice Sites, Drosophila Proteins, Animals, Genetically Modified, Genome, Insect, Transcription Initiation, Genetic
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