ArticleThe EMBO journal2012
Factor-independent transcription pausing caused by recognition of the RNA-DNA hybrid sequence.
Article in The EMBO journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
46 citing papers in PubMed, 68 citations in OpenAlex.
- Heterogeneous template-dependent transcription dynamics of T7 RNAP revealed by single-molecule imaging.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Recent advances in mycobacterial transcription: insights beyond the general pathway.Journal of bacteriology · 2025Review
- Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase.bioRxiv : the preprint server for biology · 2024Article
- An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Thermodynamic model of bacterial transcription.Physical review. E · 2022Article
- Conserved Trigger Loop Histidine of RNA Polymerase II Functions as a Positional Catalyst Primarily through Steric Effects.Biochemistry · 2021Article
- β-CASP proteins removing RNA polymerase from DNA: when a torpedo is needed to shoot a sitting duck.Nucleic acids research · 2021Review
- Two distinct pathways of RNA polymerase backtracking determine the requirement for the Trigger Loop during RNA hydrolysis.Nucleic acids research · 2021Article
- Conserved DNA sequence features underlie pervasive RNA polymerase pausing.Nucleic acids research · 2021Article
- Basic mechanisms and kinetics of pause-interspersed transcript elongation.Nucleic acids research · 2021Review
- Evolving MRSA: High-level β-lactam resistance in Staphylococcus aureus is associated with RNA Polymerase alterations and fine tuning of gene expression.PLoS pathogens · 2020Article
- High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors.Nucleic acids research · 2020Article
- Mechanisms of Transcriptional Pausing in Bacteria.Journal of molecular biology · 2019Review
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Article
- NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Non-programmed transcriptional frameshifting is common and highly RNA polymerase type-dependent.Microbial cell factories · 2018Article
- Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Pausing of transcription is an important step of regulation of gene expression in bacteria and eukaryotes. Here we uncover a factor-independent mechanism of transcription pausing, which is determined by the ability of the elongating RNA polymerase to recognize the sequence of the RNA-DNA hybrid. We show that, independently of thermodynamic stability of the elongation complex, RNA polymerase directly 'senses' the shape and/or identity of base pairs of the RNA-DNA hybrid. Recognition of the RNA-DNA hybrid sequence delays translocation by RNA polymerase, and thus slows down the nucleotide addition cycle through 'in pathway' mechanism. We show that this phenomenon is conserved among bacterial and eukaryotic RNA polymerases, and is involved in regulatory pauses, such as a pause regulating the production of virulence factors in some bacteria and a pause regulating transcription/replication of HIV-1. The results indicate that recognition of RNA-DNA hybrid sequence by multi-subunit RNA polymerases is involved in transcription regulation and may determine the overall rate of transcription elongation.
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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.