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For: Palangat M, Hittinger CT, Landick R. Downstream DNA selectively affects a paused conformation of human RNA polymerase II. J Mol Biol 2004;341:429-42. [PMID: 15276834 DOI: 10.1016/j.jmb.2004.06.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Revised: 05/25/2004] [Accepted: 06/03/2004] [Indexed: 11/17/2022]
Number Cited by Other Article(s)
1
Diao AJ, Su BG, Vos SM. Pause Patrol: Negative Elongation Factor's Role in Promoter-Proximal Pausing and Beyond. J Mol Biol 2025;437:168779. [PMID: 39241983 DOI: 10.1016/j.jmb.2024.168779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024]
2
Mora Gallardo C, Sánchez de Diego A, Martínez-A C, van Wely KHM. Interplay between splicing and transcriptional pausing exerts genome-wide control over alternative polyadenylation. Transcription 2021;12:55-71. [PMID: 34365909 PMCID: PMC8555548 DOI: 10.1080/21541264.2021.1959244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
3
Scull CE, Lucius AL, Schneider DA. The N-terminal domain of the A12.2 subunit stimulates RNA polymerase I transcription elongation. Biophys J 2021;120:1883-1893. [PMID: 33737158 DOI: 10.1016/j.bpj.2021.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/26/2021] [Accepted: 03/09/2021] [Indexed: 11/30/2022]  Open
4
Stagsted LVW, O'Leary ET, Ebbesen KK, Hansen TB. The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis in mammals. eLife 2021;10:e63088. [PMID: 33476259 PMCID: PMC7819710 DOI: 10.7554/elife.63088] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022]  Open
5
Scull CE, Clarke AM, Lucius AL, Schneider DA. Downstream sequence-dependent RNA cleavage and pausing by RNA polymerase I. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49886-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]  Open
6
Scull CE, Clarke AM, Lucius AL, Schneider DA. Downstream sequence-dependent RNA cleavage and pausing by RNA polymerase I. J Biol Chem 2019;295:1288-1299. [PMID: 31843971 DOI: 10.1074/jbc.ra119.011354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/03/2019] [Indexed: 01/12/2023]  Open
7
Mora Gallardo C, Sánchez de Diego A, Gutiérrez Hernández J, Talavera-Gutiérrez A, Fischer T, Martínez-A C, van Wely KHM. Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing. Nucleic Acids Res 2019;47:5381-5394. [PMID: 30931476 PMCID: PMC6547428 DOI: 10.1093/nar/gkz235] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/12/2022]  Open
8
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
9
Castro-Gonzalez S, Colomer-Lluch M, Serra-Moreno R. Barriers for HIV Cure: The Latent Reservoir. AIDS Res Hum Retroviruses 2018;34:739-759. [PMID: 30056745 PMCID: PMC6152859 DOI: 10.1089/aid.2018.0118] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
10
Vos SM, Farnung L, Urlaub H, Cramer P. Structure of paused transcription complex Pol II-DSIF-NELF. Nature 2018;560:601-606. [PMID: 30135580 PMCID: PMC6245578 DOI: 10.1038/s41586-018-0442-2] [Citation(s) in RCA: 262] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/17/2018] [Indexed: 11/24/2022]
11
Transcription Regulation in Archaea. J Bacteriol 2016;198:1906-1917. [PMID: 27137495 DOI: 10.1128/jb.00255-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
12
Windgassen TA, Mooney RA, Nayak D, Palangat M, Zhang J, Landick R. Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase. Nucleic Acids Res 2014;42:12707-21. [PMID: 25336618 PMCID: PMC4227799 DOI: 10.1093/nar/gku997] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
13
Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ, Landick R, Weissman JS. A pause sequence enriched at translation start sites drives transcription dynamics in vivo. Science 2014;344:1042-7. [PMID: 24789973 DOI: 10.1126/science.1251871] [Citation(s) in RCA: 253] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
14
Werner F. Molecular mechanisms of transcription elongation in archaea. Chem Rev 2013;113:8331-49. [PMID: 24024741 DOI: 10.1021/cr4002325] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
15
Kinase control prevents HIV-1 reactivation in spite of high levels of induced NF-κB activity. J Virol 2012;86:4548-58. [PMID: 22345467 DOI: 10.1128/jvi.06726-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
16
Kireeva ML, Domecq C, Coulombe B, Burton ZF, Kashlev M. Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation. J Biol Chem 2011;286:30898-30910. [PMID: 21730074 DOI: 10.1074/jbc.m111.260844] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
17
Templated nucleoside triphosphate binding to a noncatalytic site on RNA polymerase regulates transcription. Proc Natl Acad Sci U S A 2011;108:6079-84. [PMID: 21447716 DOI: 10.1073/pnas.1011274108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
18
Gan Q, Schones DE, Ho Eun S, Wei G, Cui K, Zhao K, Chen X. Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis. Genome Biol 2010;11:R42. [PMID: 20398323 PMCID: PMC2884545 DOI: 10.1186/gb-2010-11-4-r42] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 02/26/2010] [Accepted: 04/15/2010] [Indexed: 12/30/2022]  Open
19
Herbert KM, Zhou J, Mooney RA, Porta AL, Landick R, Block SM. E. coli NusG inhibits backtracking and accelerates pause-free transcription by promoting forward translocation of RNA polymerase. J Mol Biol 2010;399:17-30. [PMID: 20381500 DOI: 10.1016/j.jmb.2010.03.051] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 03/25/2010] [Accepted: 03/26/2010] [Indexed: 10/19/2022]
20
Nechooshtan G, Elgrably-Weiss M, Sheaffer A, Westhof E, Altuvia S. A pH-responsive riboregulator. Genes Dev 2009;23:2650-62. [PMID: 19933154 DOI: 10.1101/gad.552209] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
21
Rhee AC, Somerlot BH, Parimi N, Gott JM. Distinct roles for sequences upstream of and downstream from Physarum editing sites. RNA (NEW YORK, N.Y.) 2009;15:1753-1765. [PMID: 19605532 PMCID: PMC2743052 DOI: 10.1261/rna.1668309] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 06/06/2009] [Indexed: 05/28/2023]
22
Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P. Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol Cell 2009;34:710-21. [PMID: 19560423 DOI: 10.1016/j.molcel.2009.06.002] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 05/05/2009] [Accepted: 06/05/2009] [Indexed: 11/17/2022]
23
Mechanism of sequence-specific pausing of bacterial RNA polymerase. Proc Natl Acad Sci U S A 2009;106:8900-5. [PMID: 19416863 DOI: 10.1073/pnas.0900407106] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
24
Borukhov S, Nudler E. RNA polymerase: the vehicle of transcription. Trends Microbiol 2008;16:126-34. [DOI: 10.1016/j.tim.2007.12.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 12/06/2007] [Accepted: 12/06/2007] [Indexed: 10/22/2022]
25
Spitalny P, Thomm M. A polymerase III-like reinitiation mechanism is operating in regulation of histone expression in archaea. Mol Microbiol 2007;67:958-70. [PMID: 18182021 PMCID: PMC2253867 DOI: 10.1111/j.1365-2958.2007.06084.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 2006;127:941-54. [PMID: 17129781 PMCID: PMC1876690 DOI: 10.1016/j.cell.2006.11.023] [Citation(s) in RCA: 380] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 11/10/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
27
Charlet-Berguerand N, Feuerhahn S, Kong SE, Ziserman H, Conaway JW, Conaway R, Egly JM. RNA polymerase II bypass of oxidative DNA damage is regulated by transcription elongation factors. EMBO J 2006;25:5481-91. [PMID: 17110932 PMCID: PMC1679758 DOI: 10.1038/sj.emboj.7601403] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 10/04/2006] [Indexed: 12/15/2022]  Open
28
Landick R. The regulatory roles and mechanism of transcriptional pausing. Biochem Soc Trans 2006;34:1062-6. [PMID: 17073751 DOI: 10.1042/bst0341062] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
29
Nag A, Narsinh K, Kazerouninia A, Martinson HG. The conserved AAUAAA hexamer of the poly(A) signal can act alone to trigger a stable decrease in RNA polymerase II transcription velocity. RNA (NEW YORK, N.Y.) 2006;12:1534-44. [PMID: 16775304 PMCID: PMC1524889 DOI: 10.1261/rna.103206] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
30
Ederth J, Mooney RA, Isaksson LA, Landick R. Functional Interplay between the Jaw Domain of Bacterial RNA Polymerase and Allele-specific Residues in the Product RNA-binding Pocket. J Mol Biol 2006;356:1163-79. [PMID: 16405998 DOI: 10.1016/j.jmb.2005.11.080] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2005] [Revised: 11/22/2005] [Accepted: 11/23/2005] [Indexed: 11/23/2022]
31
Zhang Z, Gilmour DS. Pcf11 is a termination factor in Drosophila that dismantles the elongation complex by bridging the CTD of RNA polymerase II to the nascent transcript. Mol Cell 2006;21:65-74. [PMID: 16387654 DOI: 10.1016/j.molcel.2005.11.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 10/17/2005] [Accepted: 11/02/2005] [Indexed: 10/25/2022]
32
Braglia P, Percudani R, Dieci G. Sequence context effects on oligo(dT) termination signal recognition by Saccharomyces cerevisiae RNA polymerase III. J Biol Chem 2005;280:19551-62. [PMID: 15788403 DOI: 10.1074/jbc.m412238200] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
33
Kettenberger H, Armache KJ, Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell 2005;16:955-65. [PMID: 15610738 DOI: 10.1016/j.molcel.2004.11.040] [Citation(s) in RCA: 345] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Revised: 11/19/2004] [Accepted: 11/23/2004] [Indexed: 01/22/2023]
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