Cited by 117RNA and protein synthesis mechanismsGenomics and Chromatin DynamicsRNA Research and Splicing

The DOI matches its Crossref record; 49 of the 49 references it cites were found in a registry or an index.

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

Open access

Zamft, Bradley, Bintu, Lacramioara, Ishibashi, Toyotaka, Bustamante, Carlos·2012·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.1205063109PMC PMC3384149

Open this paper in CoChat — free account Open PDF

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1073/pnas.1205063109

Cites

49 of 49 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Entropic Elasticity of λ-Phage DNA
Bustamante, C., Marko, J. F., Siggia, E. D., & Smith, S. B. (1994) · Science · doi:10.1126/science.8079175 · Cited by 2,158
Self-citation
A Slow RNA Polymerase II Affects Alternative Splicing In Vivo
de la Mata, M., Alonso, C. R., Kadener, S., Fededa, J. P., Blaustein, M., Pelisch, F., Cramer, P., Bentley, D., & Kornblihtt, A. R. (2003) · Molecular Cell · doi:10.1016/j.molcel.2003.08.001 · Cited by 683
Transcription Against an Applied Force
Yin, H. Y., Wang, M. D., Svoboda, K., Landick, R. C., Block, S. M., & Gelles, J. (1995) · Science · doi:10.1126/science.270.5242.1653 · Cited by 584
Base composition bias might result from competition for metabolic resources
Rocha, E. P. C., & Danchin, A. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02690-2 · Cited by 481
High Guanine and Cytosine Content Increases mRNA Levels in Mammalian Cells
Kudla, G., Lipinski, L., Caffin, F., Helwak, A., & Zylicz, M. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040180 · Cited by 476
Evolution of multisubunit RNA polymerases in the three domains of life
Werner, F., & Grohmann, D. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2507 · Cited by 431
Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7.
Masters, B. S., Stohl, L. L., & Clayton, D. A. (1987) · Cell · doi:10.1016/0092-8674(87)90013-4 · Cited by 410
Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals
Artsimovitch, I., & Landick, R. C. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.13.7090 · Cited by 405
Structural basis of RNA polymerase II backtracking, arrest and reactivation
Cheung, A. C. M., & Cramer, P. (2011) · Nature · doi:10.1038/nature09785 · Cited by 373
Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
Shaevitz, J. W., Abbondanzieri, E. A., Landick, R. C., & Block, S. M. (2003) · Nature · doi:10.1038/nature02191 · Cited by 372

Show all 49 references

Sorted by citations

Coupling mRNA processing with transcription in time and space
Bentley, D. L. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3662 · Cited by 828
Codon usage is an important determinant of gene expression levels largely through its effects on transcription
Zhou, Z., Dang, Y., Zhou, M., Li, L., Yu, C., Fu, J., Chen, S., & Liu, Y. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1606724113 · Cited by 441
Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing
Saldi, T. K., Cortázar, M. A., Sheridan, R. M., & Bentley, D. L. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.04.017 · Cited by 266
Causes and consequences of RNA polymerase II stalling during transcript elongation
González, M. N., Blears, D., & Svejstrup, J. Q. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-00308-8 · Cited by 262
Optical Tweezers Analysis of DNA–Protein Complexes
Heller, I., Hoekstra, T. P., King, G. A., Peterman, E. J. G., & Wuite, G. J. L. (2014) · Chemical Reviews · doi:10.1021/cr4003006 · Cited by 212
RNA polymerase II speed: a key player in controlling and adapting transcriptome composition
Muniz, L., Nicolas, E., & Trouche, D. (2021) · The EMBO Journal · doi:10.15252/embj.2020105740 · Cited by 198
“Once assembled on the promoter, the PIC opens the DNA double strand allowing transcription initiation (Dienemann et al , 2019).”
Influential
Nucleosomal Elements that Control the Topography of the Barrier to Transcription
Bintu, L., Ishibashi, T., Dangkulwanich, M., Wu, Y.-Y., Lubkowska, L., Kashlev, M., & Bustamante, C. (2012) · Cell · doi:10.1016/j.cell.2012.10.009 · Cited by 192
Self-citation
Stochastic resetting in backtrack recovery by RNA polymerases
Roldán, É., Lisica, A., Sánchez‐Taltavull, D., & Grill, S. W. (2016) · Physical review. E · doi:10.1103/physreve.93.062411 · Cited by 192
Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism
Dangkulwanich, M., Ishibashi, T., Liu, S.-X., Kireeva, M., Lubkowska, L., Kashlev, M., & Bustamante, C. (2013) · eLife · doi:10.7554/elife.00971 · Cited by 124
Self-citation
A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure
Zhang, J., & Landick, R. C. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2015.12.009 · Cited by 136
Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9
Newman, Z. R., Young, J. M., Ingolia, N. T., & Barton, G. M. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518976113 · Cited by 118
Mechanisms of backtrack recovery by RNA polymerases I and II
Lisica, A., Engel, C., Jahnel, M., Roldán, É., Galburt, E. A., Cramer, P., & Grill, S. W. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1517011113 · Cited by 117
Enhancer RNAs in cancer: regulation, mechanisms and therapeutic potential
Lee, J., Xiong, F., & Li, W. (2020) · RNA Biology · doi:10.1080/15476286.2020.1712895 · Cited by 108
Statistics of Infima and Stopping Times of Entropy Production and Applications to Active Molecular Processes
Neri, I., Roldan, E., & Jülicher, F. (2017) · Max Planck Digital Library · Cited by 124
DNA Sequences That Interfere with Transcription: Implications for Genome Function and Stability
Belotserkovskii, B. P., Mirkin, S. M., & Hanawalt, P. C. (2013) · Chemical Reviews · doi:10.1021/cr400078y · Cited by 103
Statistics of Infima and Stopping Times of Entropy Production and Applications to Active Molecular Processes
Neri, I., Roldán, É., & Jülicher, F. (2017) · Physical Review X · doi:10.1103/physrevx.7.011019 · Cited by 103
Stochastic approach to the molecular counting problem in superresolution microscopy
Rollins, G. C., Shin, J. Y., Bustamante, C., & Pressé, S. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1408071112 · Cited by 103
Self-citation
RNA polymerase pausing and nascent RNA structure formation are linked through clamp domain movement
Hein, P., Kolb, K. E., Windgassen, T. A., Bellecourt, M. J., Darst, S., Mooney, R., & Landick, R. (2014) · Nature Structural &Molecular Biology · doi:10.1038/nsmb.2867 · Cited by 91
Co-transcriptional gene regulation in eukaryotes and prokaryotes
Shine, M., Gordon, J. M., Schärfen, L., Zigáčková, D., Herzel, L., & Neugebauer, K. M. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00706-2 · Cited by 98
U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes
Mimoso, C. A., & Adelman, K. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.03.002 · Cited by 98
Single-Molecule Analysis and Engineering of DNA Motors
Mohapatra, S., Lin, C.-T., Feng, X. A., Basu, A., & Ha, T. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00361 · Cited by 89
Dynamic turnover of paused Pol II complexes at human promotersPreprint
Erickson, B., Sheridan, R. M., Cortázar, M. A., & Bentley, D. L. (2018) · Genes & Development · doi:10.1101/gad.316810.118 · Cited by 90
Production and quantification of sesquiterpenes in Saccharomyces cerevisiae, including extraction, detection and quantification of terpene products and key related metabolites
Rodriguez, S., Kirby, J., Denby, C. M., & Keasling, J. D. (2014) · Nature Protocols · doi:10.1038/nprot.2014.132 · Cited by 85
Comparative overview of RNA polymerase II and III transcription cycles, with focus on RNA polymerase III termination and reinitiation
Arimbasseri, G. A., Rijal, K., & Maraia, R. J. (2013) · Transcription · doi:10.4161/trns.27369 · Cited by 82
Path-integral formalism for stochastic resetting: Exactly solved examples and shortcuts to confinement
Roldán, É., & Gupta, S. (2017) · Physical review. E · doi:10.1103/physreve.96.022130 · Cited by 81
Molecular Mechanisms of Transcription through Single-Molecule Experiments
Dangkulwanich, M., Ishibashi, T., Bintu, L., & Bustamante, C. (2014) · Chemical Reviews · doi:10.1021/cr400730x · Cited by 81
Self-citation
Selection on codon bias in yeast: a transcriptional hypothesis
Trotta, E. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt740 · Cited by 78
Codon-Resolution Analysis Reveals a Direct and Context-Dependent Impact of Individual Synonymous Mutations on mRNA Level
Chen, S., Li, K., Cao, W., Wang, J., Zhao, T., Huan, Q., Yang, Y., Wu, S., & Qian, W. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx229 · Cited by 75
Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates
Turowski, T. W., Petfalski, E., Goddard, B. D., French, S. L., Helwak, A., & Tollervey, D. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.06.002 · Cited by 75
The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model
Fong, N., Sheridan, R. M., Ramachandran, S., & Bentley, D. L. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.09.001 · Cited by 79
Transcription factor regulation of RNA polymerase’s torque generation capacity
Ma, J., Tan, C., Gao, X., Fulbright, R. M., Roberts, J. W., & Wang, M. D. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1807031116 · Cited by 73
Integration of mRNP formation and export
Björk, P., & Wieslander, L. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2503-3 · Cited by 71
The determinants of alternative RNA splicing in human cells
Ramanouskaya, T. V., & Grinev, V. V. (2017) · Molecular Genetics and Genomics · doi:10.1007/s00438-017-1350-0 · Cited by 75
DksA Guards Elongating RNA Polymerase against Ribosome-Stalling-Induced Arrest
Zhang, Y., Mooney, R. A., Grass, J. A., Sivaramakrishnan, P., Herman, C., Landick, R. C., & Wang, J. D. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.02.005 · Cited by 63
Transcriptional Pausing as a Mediator of Bacterial Gene Regulation
Landick, R. C. (2021) · Annual Review of Microbiology · doi:10.1146/annurev-micro-051721-043826 · Cited by 57
Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states
Bose, R., Saleem, I., & Mustoe, A. M. (2024) · Cell chemical biology · doi:10.1016/j.chembiol.2023.12.010 · Cited by 64
Transcription Regulation Through Nascent RNA Folding
Schärfen, L., & Neugebauer, K. M. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.166975 · Cited by 55
Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics
Ishibashi, T., Dangkulwanich, M., Coello, Y., Lionberger, T. A., Lubkowska, L., Ponticelli, A. S., Kashlev, M., & Bustamante, C. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1401611111 · Cited by 55
Self-citation
Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing
Zeng, Y., Fair, B. J., Zeng, H., Krishnamohan, A., Hou, Y., Hall, J. M., Ruthenburg, A. J., Li, Y., & Staley, J. P. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.11.004 · Cited by 52
Targeting RNA structures in diseases with small molecules
Shao, Y., & Zhang, Q. C. (2020) · Essays in Biochemistry · doi:10.1042/ebc20200011 · Cited by 50
Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential
Vlaming, H., Mimoso, C. A., Field, A. R., Martin, B. J. E., & Adelman, K. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00785-9 · Cited by 46
Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments
Dulin, D., Berghuis, B. A., Depken, M., & Dekker, N. H. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.08.007 · Cited by 46
Mechanisms of mRNA export
Björk, P., & Wieslander, L. (2014) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2014.04.027 · Cited by 48
Single-molecule nanometry for biological physics
Kim, H., & Ha, T. (2012) · Reports on Progress in Physics · doi:10.1088/0034-4885/76/1/016601 · Cited by 45
Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates
Gabizon, R., Lee, A., Vahedian-Movahed, H., Ebright, R. H., & Bustamante, C. (2018) · Nature Communications · doi:10.1038/s41467-018-05344-9 · Cited by 45
Self-citation
High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life
Peeri, M., & Tuller, T. (2020) · Genome biology · doi:10.1186/s13059-020-01971-y · Cited by 37
T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking
Da, L., Chao, E., Shuai, Y., Wu, S., Su, X., & Yu, J. H. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx495 · Cited by 36
Widespread non-modular overlapping codes in the coding regions*
Bergman, S., & Tuller, T. (2020) · Physical Biology · doi:10.1088/1478-3975/ab7083 · Cited by 39
Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control
Taylor, K., & Sobczak, K. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21145161 · Cited by 32
So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes
Slobodin, B., & Dikstein, R. (2020) · EMBO Reports · doi:10.15252/embr.202050799 · Cited by 30
A code for transcription elongation speed
Cohen, E., Zafrir, Z., & Tuller, T. (2018) · RNA Biology · doi:10.1080/15476286.2017.1384118 · Cited by 29
RNA helicase-dependent gene looping impacts messenger RNA processing
Terrone, S., Valat, J., Fontrodona, N., Giraud, G., Claude, J., Combe, E., Lapendry, A., Polvèche, H., Ameur, L. B., Duvermy, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac717 · Cited by 29
Introduction to Optical Tweezers: Background, System Designs, and Commercial Solutions
van Mameren, J., Wuite, G. J. L., & Heller, I. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-282-3_1 · Cited by 28
Mechanical Properties of Transcription
Sevier, S. A., & Levine, H. (2017) · Physical Review Letters · doi:10.1103/physrevlett.118.268101 · Cited by 28
Statistical Analysis of Molecular Signal Recording
Glaser, J. I., Zamft, B. M., Marblestone, A. H., Moffitt, J. R., Tyo, K. E. J., Boyden, E. S., Church, G. M., & Kording, K. P. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003145 · Cited by 27
Self-citation
Single-Molecule Studies of RNA Polymerases
Michaelis, J., & Treutlein, B. (2013) · Chemical Reviews · doi:10.1021/cr400207r · Cited by 27
RNA polymerase II pausing as a context-dependent reader of the genome
Scheidegger, A., & Nechaev, S. (2015) · Biochemistry and Cell Biology · doi:10.1139/bcb-2015-0045 · Cited by 23
Nascent RNA folding mitigates transcription-associated mutagenesisPreprint
Chen, X., Yang, J., & Zhang, J. (2015) · Genome Research · doi:10.1101/gr.195164.115 · Cited by 22
Transcriptome sequencing of Chinese and Caucasian population identifies ethnic-associated differential transcript abundance of heterogeneous nuclear ribonucleoprotein K (hnRNPK)
Li, J., Lai, K. P., Ching, A. K.-K., & Chan, T.-F. (2014) · Genomics · doi:10.1016/j.ygeno.2013.12.005 · Cited by 23
Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity
Horn, A. E., Kugel, J. F., & Goodrich, J. A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw321 · Cited by 22
Synonymous nucleotide modification of the KCNH2 gene affects both mRNA characteristics and translation of the encoded hERG ion channel
Bertalovitz, A. C., Osterbur, M. L., & McDonald, T. V. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.001805 · Cited by 22
Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces
Auboeuf, D. (2020) · Life · doi:10.3390/life10020007 · Cited by 22
A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control
Long, C., Chao, E., Da, L.-T., & Yu, J. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.05.001 · Cited by 16
Optical tweezers studies of transcription by eukaryotic RNA polymerases
Lisica, A., & Grill, S. W. (2017) · BioMolecular Concepts · doi:10.1515/bmc-2016-0028 · Cited by 18
Uncovering the mechanisms of transcription elongation by eukaryotic RNA polymerases I, II, and III
Jacobs, R. Q., Carter, Z. I., Lucius, A. L., & Schneider, D. A. (2022) · iScience · doi:10.1016/j.isci.2022.105306 · Cited by 17
Dissecting nucleotide selectivity in viral RNA polymerases
Long, C., Romero, M. E., Rocco, D. L., & Yu, J. H. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.06.005 · Cited by 18
Nucleosomal arrangement affects single-molecule transcription dynamics
Fitz, V., Shin, J., Ehrlich, C., Farnung, L., Cramer, P., Zaburdaev, V., & Grill, S. W. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1602764113 · Cited by 16
Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding
Xu, X., Jin, L., Xie, L., & Chen, S. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c01233 · Cited by 15
Oxazinomycin arrests RNA polymerase at the polythymidine sequences
Prajapati, R. K., Rosenqvist, P., Palmu, K., Mäkinen, J., Malinen, A. M., Virta, P., Metsä‐Ketelä, M., & Belogurov, G. A. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz782 · Cited by 16
Single-nucleotide control of tRNA folding cooperativity under near-cellular conditions
Leamy, K. A., Yamagami, R., Yennawar, N. H., & Bevilacqua, P. C. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1913418116 · Cited by 15
Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions
Qi, F., & Frishman, D. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx161 · Cited by 16
Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect
Yu, G., Liu, Y., Li, Z., Deng, S., Wu, Z., Zhang, X., Chen, W., Yang, J., Chen, X., & Yang, J. (2023) · Nature Communications · doi:10.1038/s41467-023-41550-w · Cited by 14
High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes
Peterman, E. L., Ploessl, D. S., Love, K. S., Sanabria, V., Daniels, R. F., Johnstone, C. P., Godavarti, D. R., Kabaria, S. R., Oakes, C. G., Pai, A. A., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf528 · Cited by 12
TEFM Enhances Transcription Elongation by Modifying mtRNAP Pausing Dynamics
Yu, H., Cheng, X., Long, M., Jia, H., Xue, G., Du, S., Coello, Y., & Ishibashi, T. (2018) · Biophysical Journal · doi:10.1016/j.bpj.2018.11.004 · Cited by 12
Self-citation
Basic mechanisms and kinetics of pause-interspersed transcript elongation
Qian, J., Dunlap, D. D., & Finzi, L. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1182 · Cited by 12
HIV-1 RNAs
Harwig, A., Das, A. T., & Berkhout, B. (2015) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000135 · Cited by 9
The thermodynamic patterns of eukaryotic genes suggest a mechanism for intron–exon recognition
Nedelcheva‐Veleva, M., Sarov, M., Yanakiev, I., Mihailovska, E., Ivanov, M. P., Panova, G., & Stoynov, S. (2013) · Nature Communications · doi:10.1038/ncomms3101 · Cited by 8
Reciprocating RNA Polymerase batters through roadblocks
Qian, J., Cartee, A., Xu, W., Yan, Y., Wang, B., Artsimovitch, I., Dunlap, D. D., & Finzi, L. (2024) · Nature Communications · doi:10.1038/s41467-024-47531-x · Cited by 8
Characterization and physical mapping of 18S and 5S ribosomal genes in Indian major carps (Pisces, Cyprinidae)
Kumar, R., Kushwaha, B., & Nagpure, N. S. (2013) · Micron · doi:10.1016/j.micron.2013.03.001 · Cited by 8
Alkaline pH has an unexpected effect on transcriptional pausing during synthesis of the Escherichia coli pH-responsive riboswitch
Stephen, C. N., & Mishanina, T. V. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102302 · Cited by 7
Introduction to Optical Tweezers: Background, System Designs, and Commercial Solutions
van Mameren, J., Wuite, G. J. L., & Heller, I. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7271-5_1 · Cited by 7
The fitness consequences of synonymous mutations in Escherichia coli: Experimental evidence for a pleiotropic effect of translational selection
Ballard, A., Bieniek, S., & Carlini, D. B. (2019) · Gene · doi:10.1016/j.gene.2019.01.031 · Cited by 8
RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcription in cis
Boots, J. L., von Pelchrzim, F., Weiss, A., Zimmermann, B., Friesacher, T., Radtke, M., Żywicki, M., Chen, D., Matylla-Kulińska, K., Žagrović, B., et al. (2020) · Transcription · doi:10.1080/21541264.2020.1790990 · Cited by 7
Introduction to Optical Tweezers: Background, System Designs, and Applications
Malinowska, A. M., van Mameren, J., Peterman, E. J. G., Wuite, G. J. L., & Heller, I. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3377-9_1 · Cited by 8
A Codon-Pair Bias Associated With Network Interactions in Influenza A, B, and C Genomes
Plant, E. P., & Ye, Z. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.699141 · Cited by 7
Residence time analysis of RNA polymerase transcription dynamics: A Bayesian sticky HMM approach
Kilic, Z., Sgouralis, I., & Pressé, S. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.02.045 · Cited by 6
Conformational Dynamics of Influenza A Virus Ribonucleoprotein Complexes during RNA Synthesis
Carlero, D., Fukuda, S., Bocanegra, R., Ando, T., Martín‐Benito, J., & Ibarra, B. (2024) · ACS Nano · doi:10.1021/acsnano.4c01362 · Cited by 5
CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing
Shenasa, H., Fong, N., Erickson, B., Iosub, I. A., Ule, J., & Bentley, D. L. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2504034122 · Cited by 4
Reaction dynamics under confinement: an exact path integral treatment of a two-stage model of stochastic gene expression
SHARMA, R. R., & Cherayil, B. J. (2013) · Journal of Statistical Mechanics Theory and Experiment · doi:10.1088/1742-5468/2013/10/p10029 · Cited by 5
Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast
Lukačišin, M., Landon, M., & Jajoo, R. (2017) · PLOS ONE · doi:10.1371/journal.pone.0174066 · Cited by 4
The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate
Hyder, U., & Bentley, D. L. (2026) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051424-053703 · Cited by 5
Kinetic pathway of HIV-1 TAR cotranscriptional folding
Jin, L., Zhang, S., Song, Z., Heng, X., & Chen, S. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae362 · Cited by 4
A Single-Molecule View on Cellular and Viral RNA Synthesis
Ostrofet, E., Papini, F. S., Malinen, A. M., & Dulin, D. (2019) · Biological and medical physics, biomedical engineering · doi:10.1007/978-1-4939-9726-8_6 · Cited by 5
Single molecule studies of RNA polymerase II transcription in vitro
Horn, A. E., Goodrich, J. A., & Kugel, J. F. (2014) · Transcription · doi:10.4161/trns.27608 · Cited by 4
Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data
Liu, L., Zhao, Y., Hassett, R., Toneyan, S., Koo, P. K., & Siepel, A. C. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf092 · Cited by 3
Profiling of Nascent Lariat Intermediates Reveals Key Genetic Determinants of the Timing of Human Co-transcriptional SplicingPreprint
Zeng, Y., Zeng, H., Fair, B. J., Krishnamohan, A., Hou, Y., Hall, J. M., Ruthenburg, A. J., Li, Y., & Staley, J. P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.18.464728 · Cited by 3
Regulation of RNA transcript elongation in metazoans and its relevance to disease
Mimoso, C. A., Fianu, I., & Adelman, K. (2026) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-026-01003-w · Cited by 2
Analytic delay distributions for a family of gene transcription models
Hosseini, S. H., & Roussel, M. R. (2024) · Mathematical Biosciences & Engineering · doi:10.3934/mbe.2024273 · Cited by 2
Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3’ splice sites
Herbert, A., Hatfield, A., Randazza, A., Miyamoto, V., Palmer, K., & Lackey, L. (2025) · RNA Biology · doi:10.1080/15476286.2025.2570043 · Cited by 2
The role of RNA structure in 3’ end processing in eukaryotes
Xu, J., Duncan, S. H., & Ding, Y. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102933 · Cited by 3

Authors: Zamft, B., Bintu, L., Ishibashi, T., & Bustamante, C.
Affiliations: University of California, Berkeley (US)
Howard Hughes Medical Institute (US)
Corresponding author: Bustamante, Carlos
ORCID: Bintu, Lacramioara
Ishibashi, Toyotaka
Bustamante, Carlos
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 2012-05-21
Volume: 109
Issue: 23
Pages: 8948-8953
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.1205063109
PMC: PMC3384149
OpenAlex: W2129738296
Cited by: 117
References: 49
Citations by year: 2026: 3 · 2025: 8 · 2024: 7 · 2023: 4 · 2022: 8 · 2021: 7 · 2020: 14 · 2019: 9 · 2018: 6 · 2017: 14 · 2016: 9 · 2015: 5 · 2014: 11 · 2013: 9 · 2012: 2
FWCI: 3.47
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
Funders: Howard Hughes Medical Institute
U.S. Department of Energy (DEAC03-76SF00098)
National Institutes of Health
Japan Society for the Promotion of Science
National Institute of General Medical Sciences (R01-GM0325543)
Lawrence Berkeley National Laboratory
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords: RNA polymerase pausing, RNA polymerase II, transcription elongation, backtracking, ribonuclease, kinetic model, cis-acting regulation
MeSH terms: Base Composition, Computer Simulation, Models, Biological, Oligonucleotides, RNA, RNA Polymerase II, DNA-Directed RNA Polymerases, Saccharomyces cerevisiae, Transcription, Genetic, Polymerase Chain Reaction, Myxococcus xanthus, Mitochondrial Proteins, Saccharomyces cerevisiae Proteins, RNA Folding

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks