ArticleNucleic acids research2018
RNA-DNA and DNA-DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 20 citations in OpenAlex.
- Discovering, Integrating, and Reinterpreting the Molecular Logic of Life: From Classical Theories of Heredity to an Extended Functional Perspective on the Central Dogma.Life (Basel, Switzerland) · 2026Review
- Archaeal RNA processing and regulation: expanding the functional landscape.Microbiology and molecular biology reviews : MMBR · 2025Review
- The relevance of RNA-DNA interactions as regulators of physiological functions.Pflugers Archiv : European journal of physiology · 2025Review
- NusG-Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression.Journal of molecular biology · 2025Review
- Robust regulation of transcription pausing inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- First passage time study of DNA strand displacement.Biophysical journal · 2021Article
- Basic mechanisms and kinetics of pause-interspersed transcript elongation.Nucleic acids research · 2021Review
- Bayesian inference and comparison of stochastic transcription elongation models.PLoS computational biology · 2020Article
- Oxazinomycin arrests RNA polymerase at the polythymidine sequences.Nucleic acids research · 2019Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase.Journal of molecular biology · 2019Article
- RNA Polymerase Clamp Movement Aids Dissociation from DNA but Is Not Required for RNA Release at Intrinsic Terminators.Journal of molecular biology · 2019Article
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7 authors at 2 institutions in 1 country.
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Abstract
Translocation of RNA polymerase (RNAP) along DNA may be rate-limiting for transcription elongation. The Brownian ratchet model posits that RNAP rapidly translocates back and forth until the post-translocated state is stabilized by NTP binding. An alternative model suggests that RNAP translocation is slow and poorly reversible. To distinguish between these two models, we take advantage of an observation that pyrophosphorolysis rates directly correlate with the abundance of the pre-translocated fraction. Pyrophosphorolysis by RNAP stabilized in the pre-translocated state by bacteriophage HK022 protein Nun was used as a reference point to determine the pre-translocated fraction in the absence of Nun. The stalled RNAP preferentially occupies the post-translocated state. The forward translocation rate depends, among other factors, on melting of the RNA-DNA base pair at the upstream edge of the transcription bubble. DNA-DNA base pairing immediately upstream from the RNA-DNA hybrid stabilizes the post-translocated state. This mechanism is conserved between E. coli RNAP and S. cerevisiae RNA polymerase II and is partially dependent on the lid domain of the catalytic subunit. Thus, the RNA-DNA hybrid and DNA reannealing at the upstream edge of the transcription bubble emerge as targets for regulation of the transcription elongation rate.
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