ArticleProceedings of the National Academy of Sciences of the United States of America2023
An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- RNA polymerase inhibitors reveal active-site motions essential for the nucleotide addition cycle.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Structural basis for loading of transcription repair-coupling factor Mfd onto stalled elongation complexes.Nucleic acids research · 2026Article
- Apical localization of RNA polymerases modulates transcription dynamics and supercoiling domains revealed by cryo-ET.Molecular cell · 2026Article
- Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity.Molecular cell · 2026Article
- ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition.bioRxiv : the preprint server for biology · 2026Article
- RNAP-seq:bioRxiv : the preprint server for biology · 2026Article
- Structural principles of transcriptional collisions.bioRxiv : the preprint server for biology · 2026Article
- Apical Localization of RNA Polymerases Modulate Transcription Dynamics and Supercoiling Domains Revealed by Cryo-ET.bioRxiv : the preprint server for biology · 2026Article
- RNA polymerase inhibitors reveal active-site motions essential for the nucleotide-addition cycle.bioRxiv : the preprint server for biology · 2026Article
- Structural basis of pausing during transcription initiation in mycobacterium tuberculosis.Nature communications · 2026Article
- Nucleic Acid Sequence Determinants of Transcriptional Pausing by the Human Mitochondrial RNA Polymerase (POLRMT).Biochemistry · 2025Article
- Structural basis for loading of Transcription Repair-Coupling factor Mfd onto stalled elongation complexes.bioRxiv : the preprint server for biology · 2025Article
- A large-scale curated and filterable dataset for cryo-EM foundation model pre-training.Scientific data · 2025Article
- Peering into the Bacterial Cell: From Transcription to Functional Genomics.Journal of molecular biology · 2025Review
- Single-stranded DNA drives σ subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations.Nucleic acids research · 2025Article
- RapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation.Nature structural & molecular biology · 2025Article
- Single-molecule studies reveal the off-pathway early paused state intermediates as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors.Nucleic acids research · 2025Article
- RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease.Journal of molecular biology · 2025Review
- NusG-Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression.Journal of molecular biology · 2025Review
- The yin and yang of the universal transcription factor NusG.Current opinion in microbiology · 2024Review
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8 authors.
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Abstract
Transcriptional pausing underpins the regulation of cellular RNA synthesis, but its mechanism remains incompletely understood. Sequence-specific interactions of DNA and RNA with the dynamic, multidomain RNA polymerase (RNAP) trigger reversible conformational changes at pause sites that temporarily interrupt the nucleotide addition cycle. These interactions initially rearrange the elongation complex (EC) into an elemental paused EC (ePEC). ePECs can form longer-lived PECs by further rearrangements or interactions of diffusible regulators. For both bacterial and mammalian RNAPs, a half-translocated state in which the next DNA template base fails to load into the active site appears central to the ePEC. Some RNAPs also swivel interconnected modules that may stabilize the ePEC. However, it is unclear whether swiveling and half-translocation are requisite features of a single ePEC state or if multiple ePEC states exist. Here, we use cryo-electron microscopy (cryo-EM) analysis of ePECs with different RNA-DNA sequences combined with biochemical probes of ePEC structure to define an interconverting ensemble of ePEC states. ePECs occupy either pre- or half-translocated states but do not always swivel, indicating that difficulty in forming the posttranslocated state at certain RNA-DNA sequences may be the essence of the ePEC. The existence of multiple ePEC conformations has broad implications for transcriptional regulation.
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