ArticleNature structural & molecular biology2014
RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement.
Article in Nature structural & molecular biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed.
- Characterization of Hairpin Loops and Cruciforms Across 118,019 Genomes Spanning the Tree of Life.Genome biology and evolution · 2026Article
- 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
- Structural Insights into De Novo Promoter Escape by Mycobacterium tuberculosis RNA Polymerase.Nature communications · 2025Article
- Widespread epistasis shapes RNA polymerase II active site function and evolution.Nature communications · 2025Article
- Applying the brakes to transcription: regulation of gene expression by RNA polymerase pausing.Journal of bacteriology · 2025Review
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis.Molecular cell · 2025Article
- Clues to transcription/replication collision-induced DNA damage: it was RNAP, in the chromosome, with the fork.FEBS letters · 2025Review
- Thiolutin has complex effects in vivo but is a direct inhibitor of RNA polymerase II in vitro.Nucleic acids research · 2024Article
- Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand.Nature structural & molecular biology · 2023Article
- Article
- 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
- Isolation of E. coli RNA polymerase transcription elongation complexes by selective solid-phase photoreversible immobilization.Methods in enzymology · 2023Article
- Article
- Evolution of the RNA Cleavage Subunit C11/RPC10, and Recycling by RNA Polymerase III.Journal of cellular immunology · 2022Article
- Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Monitoring RNA dynamics in native transcriptional complexes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Transcription complexes as RNA chaperones.Transcription · 2021Article
- RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding.Nucleic acids research · 2021Article
- CoBold: a method for identifying different functional classes of transient RNA structure features that can impact RNA structure formation in vivo.Nucleic acids research · 2021Article
10 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
The rates of RNA synthesis and the folding of nascent RNA into biologically active structures are linked via pausing by RNA polymerase (RNAP). Structures that form within the RNA-exit channel can either increase pausing by interacting with RNAP or decrease pausing by preventing backtracking. Conversely, pausing is required for proper folding of some RNAs. Opening of the RNAP clamp domain has been proposed to mediate some effects of nascent-RNA structures. However, the connections among RNA structure formation and RNAP clamp movement and catalytic activity remain uncertain. Here, we assayed exit-channel structure formation in Escherichia coli RNAP with disulfide cross-links that favor closed- or open-clamp conformations and found that clamp position directly influences RNA structure formation and RNAP catalytic activity. We report that exit-channel RNA structures slow pause escape by favoring clamp opening through interactions with the flap that slow translocation.
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