ArticleeLife2013
Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism.
Article in eLife, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
- Structural dynamics of RNA polymerase II throughout the nucleotide addition cycle.Nature communications · 2026Article
- Structural Dynamics of RNA Polymerase II During Nucleotide Addition Cycle.bioRxiv : the preprint server for biology · 2026Article
- Large RNA polymerase II condensates are promoter-centric assemblies associated with early stages of transcription at all expressed genes.bioRxiv : the preprint server for biology · 2026Article
- Braess' Paradox in Enzyme Kinetics: Asymmetry from Population Balance without Direct Cooperativity.Journal of chemical theory and computation · 2026Article
- Ribosomal RNA synthesis by RNA polymerase I is subject to premature termination of transcription.eLife · 2026Article
- The PARP1-EXD2 axis orchestrates R-loop resolution to safeguard genome stability.Nature chemical biology · 2026Article
- Widespread epistasis shapes RNA polymerase II active site function and evolution.Nature communications · 2025Article
- Transcription-Coupled Template Reconfiguration of 8-Oxoguanine for Error-Prone Transcription Revealed by Time-Resolved X-ray Crystallography and Molecular Dynamics.Journal of the American Chemical Society · 2025Article
- Article
- RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease.Journal of molecular biology · 2025Review
- NTPs compete in the active site of RNA polymerases I and II.Biophysical chemistry · 2024Article
- Article
- Higher-order epistasis within Pol II trigger loop haplotypes.bioRxiv : the preprint server for biology · 2024Article
- Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Transcription elongation of the plant RNA polymerase IV is prone to backtracking.Science advances · 2024Article
- Conformational Dynamics of Influenza A Virus Ribonucleoprotein Complexes during RNA Synthesis.ACS nano · 2024Article
- Reversible Kinetics in Multi-nucleotide Addition Catalyzed by S. cerevisiae RNA polymerase II Reveal Slow Pyrophosphate Release.Journal of molecular biology · 2024Article
- DNA-directed termination of RNA polymerase II transcription.Molecular cell · 2023Article
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- Transient-State Kinetic Analysis of the RNA Polymerase II Nucleotide Incorporation Mechanism.Biochemistry · 2023Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on byOn the move.2013
Authors and funding
7 authors.
Funding
Abstract
During transcription elongation, RNA polymerase has been assumed to attain equilibrium between pre- and post-translocated states rapidly relative to the subsequent catalysis. Under this assumption, recent single-molecule studies proposed a branched Brownian ratchet mechanism that necessitates a putative secondary nucleotide binding site on the enzyme. By challenging individual yeast RNA polymerase II with a nucleosomal barrier, we separately measured the forward and reverse translocation rates. Surprisingly, we found that the forward translocation rate is comparable to the catalysis rate. This finding reveals a linear, non-branched ratchet mechanism for the nucleotide addition cycle in which translocation is one of the rate-limiting steps. We further determined all the major on- and off-pathway kinetic parameters in the elongation cycle. The resulting translocation energy landscape shows that the off-pathway states are favored thermodynamically but not kinetically over the on-pathway states, conferring the enzyme its propensity to pause and furnishing the physical basis for transcriptional regulation. DOI:http://dx.doi.org/10.7554/eLife.00971.001.
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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.