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For: Bai L, Shundrovsky A, Wang MD. Sequence-dependent kinetic model for transcription elongation by RNA polymerase. J Mol Biol 2004;344:335-49. [PMID: 15522289 DOI: 10.1016/j.jmb.2004.08.107] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Revised: 08/06/2004] [Accepted: 08/06/2004] [Indexed: 11/16/2022]
Number Cited by Other Article(s)
1
Fang C, Huang K, Wu X, Zhang H, Gu Z, Wang J, Zhang Y. Transcription elongation of the plant RNA polymerase IV is prone to backtracking. SCIENCE ADVANCES 2024;10:eadq3087. [PMID: 39178250 PMCID: PMC11343019 DOI: 10.1126/sciadv.adq3087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/22/2024] [Indexed: 08/25/2024]
2
Nova IC, Craig JM, Mazumder A, Laszlo AH, Derrington IM, Noakes MT, Brinkerhoff H, Yang S, Vahedian-Movahed H, Li L, Zhang Y, Bowman JL, Huang JR, Mount JW, Ebright RH, Gundlach JH. Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase. Proc Natl Acad Sci U S A 2024;121:e2321017121. [PMID: 38990947 PMCID: PMC11260103 DOI: 10.1073/pnas.2321017121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/23/2024] [Indexed: 07/13/2024]  Open
3
Hosseini SH, Roussel MR. Analytic delay distributions for a family of gene transcription models. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024;21:6225-6262. [PMID: 39176425 DOI: 10.3934/mbe.2024273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
4
Midha T, Mallory JD, Kolomeisky AB, Igoshin OA. Synergy among Pausing, Intrinsic Proofreading, and Accessory Proteins Results in Optimal Transcription Speed and Tolerable Accuracy. J Phys Chem Lett 2023;14:3422-3429. [PMID: 37010247 DOI: 10.1021/acs.jpclett.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
5
Johnson RS, Strausbauch M, McCloud C. An NTP-driven mechanism for the nucleotide addition cycle of Escherichia coli RNA polymerase during transcription. PLoS One 2022;17:e0273746. [PMID: 36282801 PMCID: PMC9595533 DOI: 10.1371/journal.pone.0273746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/15/2022] [Indexed: 11/06/2022]  Open
6
Qian J, Dunlap D, Finzi L. Thermodynamic model of bacterial transcription. Phys Rev E 2022;106:044406. [PMID: 36397483 PMCID: PMC9803584 DOI: 10.1103/physreve.106.044406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/20/2022] [Indexed: 01/03/2023]
7
Kor R, Mohammad-Rafiee F. Theoretical study of RNA-polymerase behavior considering the backtracking state. SOFT MATTER 2022;18:5979-5988. [PMID: 35920142 DOI: 10.1039/d2sm00232a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
8
Plaskon D, Evensen C, Henderson K, Palatnik B, Ishikuri T, Wang HC, Doughty S, Thomas Record M. Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis. J Mol Biol 2022;434:167621. [DOI: 10.1016/j.jmb.2022.167621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
9
Sahoo M, N A, Baral PR, Klumpp S. Accuracy and speed of elongation in a minimal model of DNA replication. Phys Rev E 2021;104:034417. [PMID: 34654207 DOI: 10.1103/physreve.104.034417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/08/2021] [Indexed: 11/07/2022]
10
Landick R. Transcriptional Pausing as a Mediator of Bacterial Gene Regulation. Annu Rev Microbiol 2021;75:291-314. [PMID: 34348029 DOI: 10.1146/annurev-micro-051721-043826] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
11
Kilic Z, Sgouralis I, Pressé S. Residence time analysis of RNA polymerase transcription dynamics: A Bayesian sticky HMM approach. Biophys J 2021;120:1665-1679. [PMID: 33705761 DOI: 10.1016/j.bpj.2021.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 01/09/2023]  Open
12
Qian J, Dunlap D, Finzi L. Basic mechanisms and kinetics of pause-interspersed transcript elongation. Nucleic Acids Res 2021;49:15-24. [PMID: 33330935 PMCID: PMC7797061 DOI: 10.1093/nar/gkaa1182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022]  Open
13
Yang D, Liu W, Deng X, Xie W, Chen H, Zhong Z, Ma J. GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid Duplexes. Biophys J 2020;119:852-861. [PMID: 32738216 DOI: 10.1016/j.bpj.2020.06.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/22/2020] [Accepted: 06/18/2020] [Indexed: 01/25/2023]  Open
14
Gaspard P. Template-directed growth of copolymers. CHAOS (WOODBURY, N.Y.) 2020;30:043114. [PMID: 32357651 DOI: 10.1063/1.5145100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
15
Nakajima RT, Costa PR, Lemke N. Cooperative and sequence-dependent model for RNAP dynamics: Application to ribosomal gene transcription. J Theor Biol 2020;488:110134. [PMID: 31874133 DOI: 10.1016/j.jtbi.2019.110134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/11/2019] [Accepted: 12/19/2019] [Indexed: 11/29/2022]
16
Douglas J, Kingston R, Drummond AJ. Bayesian inference and comparison of stochastic transcription elongation models. PLoS Comput Biol 2020;16:e1006717. [PMID: 32059006 PMCID: PMC7046298 DOI: 10.1371/journal.pcbi.1006717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/27/2020] [Accepted: 12/13/2019] [Indexed: 02/06/2023]  Open
17
Prajapati RK, Rosenqvist P, Palmu K, Mäkinen JJ, Malinen AM, Virta P, Metsä-Ketelä M, Belogurov GA. Oxazinomycin arrests RNA polymerase at the polythymidine sequences. Nucleic Acids Res 2019;47:10296-10312. [PMID: 31495891 PMCID: PMC6821320 DOI: 10.1093/nar/gkz782] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/13/2019] [Accepted: 08/31/2019] [Indexed: 02/06/2023]  Open
18
Kang JY, Mishanina TV, Landick R, Darst SA. Mechanisms of Transcriptional Pausing in Bacteria. J Mol Biol 2019;431:4007-4029. [PMID: 31310765 DOI: 10.1016/j.jmb.2019.07.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 12/21/2022]
19
Belogurov GA, Artsimovitch I. The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase. J Mol Biol 2019;431:3975-4006. [PMID: 31153902 DOI: 10.1016/j.jmb.2019.05.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/15/2022]
20
Long C, E. C, Da LT, Yu J. A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control. Comput Struct Biotechnol J 2019;17:638-644. [PMID: 31193497 PMCID: PMC6535458 DOI: 10.1016/j.csbj.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/25/2019] [Accepted: 05/04/2019] [Indexed: 12/02/2022]  Open
21
Belitsky V, Schütz G. RNA Polymerase interactions and elongation rate. J Theor Biol 2019;462:370-380. [DOI: 10.1016/j.jtbi.2018.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 11/30/2022]
22
Transcription factor regulation of RNA polymerase's torque generation capacity. Proc Natl Acad Sci U S A 2019;116:2583-2588. [PMID: 30635423 DOI: 10.1073/pnas.1807031116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
23
Saba J, Chua XY, Mishanina TV, Nayak D, Windgassen TA, Mooney RA, Landick R. The elemental mechanism of transcriptional pausing. eLife 2019;8:e40981. [PMID: 30618376 PMCID: PMC6336406 DOI: 10.7554/elife.40981] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/19/2018] [Indexed: 12/20/2022]  Open
24
Belitsky V, Schütz GM. Stationary RNA polymerase fluctuations during transcription elongation. Phys Rev E 2019;99:012405. [PMID: 30780341 DOI: 10.1103/physreve.99.012405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Indexed: 06/09/2023]
25
Turtola M, Mäkinen JJ, Belogurov GA. Active site closure stabilizes the backtracked state of RNA polymerase. Nucleic Acids Res 2018;46:10870-10887. [PMID: 30256972 PMCID: PMC6237748 DOI: 10.1093/nar/gky883] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/30/2018] [Accepted: 09/19/2018] [Indexed: 01/02/2023]  Open
26
Le TT, Wang MD. Molecular Highways—Navigating Collisions of DNA Motor Proteins. J Mol Biol 2018;430:4513-4524. [DOI: 10.1016/j.jmb.2018.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 01/09/2023]
27
Unarta IC, Zhu L, Tse CKM, Cheung PPH, Yu J, Huang X. Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models. Curr Opin Struct Biol 2018;49:54-62. [PMID: 29414512 DOI: 10.1016/j.sbi.2018.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022]
28
Le TT, Yang Y, Tan C, Suhanovsky MM, Fulbright RM, Inman JT, Li M, Lee J, Perelman S, Roberts JW, Deaconescu AM, Wang MD. Mfd Dynamically Regulates Transcription via a Release and Catch-Up Mechanism. Cell 2017;172:344-357.e15. [PMID: 29224782 DOI: 10.1016/j.cell.2017.11.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/21/2017] [Accepted: 11/09/2017] [Indexed: 11/25/2022]
29
Mellenius H, Ehrenberg M. Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase. Nucleic Acids Res 2017;45:11582-11593. [PMID: 29036494 PMCID: PMC5714138 DOI: 10.1093/nar/gkx849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/10/2017] [Accepted: 09/22/2017] [Indexed: 01/01/2023]  Open
30
Gaspard P. Iterated function systems for DNA replication. Phys Rev E 2017;96:042403. [PMID: 29347611 DOI: 10.1103/physreve.96.042403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Indexed: 06/07/2023]
31
Mustaev A, Roberts J, Gottesman M. Transcription elongation. Transcription 2017;8:150-161. [PMID: 28301288 PMCID: PMC5501382 DOI: 10.1080/21541264.2017.1289294] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 12/23/2022]  Open
32
Lukačišin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One 2017;12:e0174066. [PMID: 28301878 PMCID: PMC5354634 DOI: 10.1371/journal.pone.0174066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 03/02/2017] [Indexed: 01/22/2023]  Open
33
Gaspard P. Template-Directed Copolymerization, Random Walks along Disordered Tracks, and Fractals. PHYSICAL REVIEW LETTERS 2016;117:238101. [PMID: 27982621 DOI: 10.1103/physrevlett.117.238101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Indexed: 06/06/2023]
34
Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences. Proc Natl Acad Sci U S A 2016;113:E7409-E7417. [PMID: 27830653 DOI: 10.1073/pnas.1607760113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
35
Xu H, Skinner SO, Sokac AM, Golding I. Stochastic Kinetics of Nascent RNA. PHYSICAL REVIEW LETTERS 2016;117:128101. [PMID: 27667861 PMCID: PMC5033037 DOI: 10.1103/physrevlett.117.128101] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
36
Zhang J, Landick R. A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure. Trends Biochem Sci 2016;41:293-310. [PMID: 26822487 DOI: 10.1016/j.tibs.2015.12.009] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 02/06/2023]
37
Bordoy AE, Chatterjee A. Cis-Antisense Transcription Gives Rise to Tunable Genetic Switch Behavior: A Mathematical Modeling Approach. PLoS One 2015. [PMID: 26222133 PMCID: PMC4519249 DOI: 10.1371/journal.pone.0133873] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
38
Skancke J, Bar N, Kuiper M, Hsu LM. Sequence-Dependent Promoter Escape Efficiency Is Strongly Influenced by Bias for the Pretranslocated State during Initial Transcription. Biochemistry 2015;54:4267-75. [PMID: 26083830 DOI: 10.1021/acs.biochem.5b00272] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
39
Imashimizu M, Takahashi H, Oshima T, McIntosh C, Bubunenko M, Court DL, Kashlev M. Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo. Genome Biol 2015;16:98. [PMID: 25976475 PMCID: PMC4457086 DOI: 10.1186/s13059-015-0666-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/05/2015] [Indexed: 01/17/2023]  Open
40
DNA template dependent accuracy variation of nucleotide selection in transcription. PLoS One 2015;10:e0119588. [PMID: 25799551 PMCID: PMC4370716 DOI: 10.1371/journal.pone.0119588] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/06/2015] [Indexed: 11/19/2022]  Open
41
Mejia YX, Nudler E, Bustamante C. Trigger loop folding determines transcription rate of Escherichia coli's RNA polymerase. Proc Natl Acad Sci U S A 2015;112:743-8. [PMID: 25552559 PMCID: PMC4311812 DOI: 10.1073/pnas.1421067112] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
42
Yu J, Da LT, Huang X. Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle. Phys Biol 2014;12:016004. [DOI: 10.1088/1478-3975/12/1/016004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
43
Fange D, Mellenius H, Dennis PP, Ehrenberg M. Thermodynamic modeling of variations in the rate of RNA chain elongation of E. coli rrn operons. Biophys J 2014;106:55-64. [PMID: 24411237 DOI: 10.1016/j.bpj.2013.11.4487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 11/07/2013] [Accepted: 11/25/2013] [Indexed: 11/15/2022]  Open
44
Vvedenskaya IO, Vahedian-Movahed H, Bird JG, Knoblauch JG, Goldman SR, Zhang Y, Ebright RH, Nickels BE. Interactions between RNA polymerase and the "core recognition element" counteract pausing. Science 2014;344:1285-9. [PMID: 24926020 DOI: 10.1126/science.1253458] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
45
Dangkulwanich M, Ishibashi T, Bintu L, Bustamante C. Molecular mechanisms of transcription through single-molecule experiments. Chem Rev 2014;114:3203-23. [PMID: 24502198 PMCID: PMC3983126 DOI: 10.1021/cr400730x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Indexed: 01/02/2023]
46
Yuzenkova Y, Roghanian M, Bochkareva A, Zenkin N. Tagetitoxin inhibits transcription by stabilizing pre-translocated state of the elongation complex. Nucleic Acids Res 2013;41:9257-65. [PMID: 23935117 PMCID: PMC3814378 DOI: 10.1093/nar/gkt708] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/16/2013] [Accepted: 07/18/2013] [Indexed: 01/30/2023]  Open
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External conditions inversely change the RNA polymerase II elongation rate and density in yeast. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013;1829:1248-55. [PMID: 24103494 DOI: 10.1016/j.bbagrm.2013.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/25/2013] [Accepted: 09/30/2013] [Indexed: 11/23/2022]
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Intermittent Transcription Dynamics for the Rapid Production of Long Transcripts of High Fidelity. Cell Rep 2013;5:521-30. [DOI: 10.1016/j.celrep.2013.09.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 02/01/2013] [Accepted: 09/05/2013] [Indexed: 11/23/2022]  Open
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Forties RA, Ma J, Wang MD. On the move. eLife 2013;2:e01414. [PMID: 24073329 PMCID: PMC3782732 DOI: 10.7554/elife.01414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
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Dangkulwanich M, Ishibashi T, Liu S, Kireeva ML, Lubkowska L, Kashlev M, Bustamante CJ. Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. eLife 2013;2:e00971. [PMID: 24066225 PMCID: PMC3778554 DOI: 10.7554/elife.00971] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/13/2013] [Indexed: 12/31/2022]  Open
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