Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila
Open accessAbstract
To Stall or Not to Stall: Recent studies in mammals and Drosophila have shown that RNA polymerase II frequently stalls shortly after initiating messenger RNA synthesis and that this stalling is important for proper expression of genes. Although several protein factors that affect polymerase stalling are known, the role of DNA sequence in this process has remained unclear. Now Nechaev et al. (p. 335 , published online 10 December) report that the initially transcribed sequences of many genes contain a signal that works like a stop sign for the elongating polymerase. Expression of genes may thus be regulated by a combination of a DNA signal that induces promoter-proximal stalling and protein factors that alter its duration.
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RNA polymerase II temporarily halts during transcript elongation, a pause stabilized by NELF and DSIF.
“It is now well-known that RNA polymerase II temporarily halts during transcript elongation, a pause stabilized by the negative elongation factor (NELF) and the 5,6-Dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) sensitivity-inducing factor (DSIF) (Nechaev et al. 2010).”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Nechaev et al. 2010
The passage labeled Abstract (page unavailable) says transient Pol II stalling is a general feature of early elongation and that NELF enhances the duration of intrinsic pauses. It does not mention DSIF or support attributing stabilization of the pause to DSIF. (LLM, conf=0.88)
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- Authors
- Nechaev, S., Fargo, D. C., dos Santos, G., Liu, L., Gao, Y., & Adelman, K.
- Affiliations
- National Institute of Environmental Health Sciences (US)
- National Institutes of Health (US)
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
- Virginia Commonwealth University (US)
- Corresponding author
- Adelman, Karen
- Venue
- Science
- Published
- 2010-01-15
- Volume
- 327
- Issue
- 5963
- Pages
- 335-338
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3435875
- OpenAlex
- W2045847295
- Cited by
- 424
- References
- 0
- Citations by year
- 2026: 15 · 2025: 14 · 2024: 19 · 2023: 18 · 2022: 19 · 2021: 18 · 2020: 18 · 2019: 40 · 2018: 20 · 2017: 28 · 2016: 23 · 2015: 25 · 2014: 30 · 2013: 35 · 2012: 41
- FWCI
- 13.70
- 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
- National Institutes of Health
- National Institute of Environmental Health Sciences (ZIAES101987, Z01ES101987)
- 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 › RNA and protein synthesis mechanisms
- Keywords
- RNA polymerase II stalling, transcription elongation, small RNA, Drosophila, backtracking, nucleotide composition, gene expression regulation
- MeSH terms
- Animals, Base Composition, Cell Line, Drosophila melanogaster, Gene Expression Regulation, Promoter Regions, Genetic, RNA, RNA Caps, RNA Polymerase II, RNA, Messenger, Transcription, Genetic, Genes, Insect, Oligonucleotide Array Sequence Analysis, Transcription Initiation Site, Genome, Insect
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