ArticleProceedings of the National Academy of Sciences of the United States of America2012
Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
What it found
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Who cites it
75 citing papers in PubMed, 117 citations in OpenAlex.
- Regulation of RNA transcript elongation in metazoans and its relevance to disease.Nature reviews. Molecular cell biology · 2026Review
- Single-Molecule Methods to Investigate Mechanisms of Transcription by RNA Polymerase ofbioRxiv : the preprint server for biology · 2026Article
- Co-transcriptional gene regulation in plants.aBIOTECH · 2026Review
- 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
- Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3' splice sites.RNA biology · 2025Article
- Targeted RNA Degradation as a Promising Therapeutic Strategy.International journal of molecular sciences · 2025Review
- CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes.Nucleic acids research · 2025Article
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.Nucleic acids research · 2025Article
- Conformational Dynamics of Influenza A Virus Ribonucleoprotein Complexes during RNA Synthesis.ACS nano · 2024Article
- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
- Kinetic pathway of HIV-1 TAR cotranscriptional folding.Nucleic acids research · 2024Article
- Reciprocating RNA Polymerase batters through roadblocks.Nature communications · 2024Article
- Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states.Cell chemical biology · 2024Review
- DNA-sequence and epigenomic determinants of local rates of transcription elongation.bioRxiv : the preprint server for biology · 2023Article
- Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect.Nature communications · 2023Article
- U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes.Molecular cell · 2023Article
- Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing.Molecular cell · 2022Article
- Uncovering the mechanisms of transcription elongation by eukaryotic RNA polymerases I, II, and III.iScience · 2022Article
- The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model.Molecular cell · 2022Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
RNA polymerase pausing represents an important mechanism of transcriptional regulation. In this study, we use a single-molecule transcription assay to investigate the effect of template base-pair composition on pausing by RNA polymerase II and the evolutionarily distinct mitochondrial polymerase Rpo41. For both enzymes, pauses are shorter and less frequent on GC-rich templates. Significantly, incubation with RNase abolishes the template dependence of pausing. A kinetic model, wherein the secondary structure of the nascent RNA poses an energetic barrier to pausing by impeding backtracking along the template, quantitatively predicts the pause densities and durations observed. The energy barriers extracted from the data correlate well with RNA folding energies obtained from cotranscriptional folding simulations. These results reveal that RNA secondary structures provide a cis-acting mechanism by which sequence modulates transcriptional 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.