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For: Zhang C, Yan H, Burton ZF. Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor II. J Biol Chem 2003;278:50101-11. [PMID: 14506279 DOI: 10.1074/jbc.m307590200] [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] [Indexed: 11/06/2022]  Open
Number Cited by Other Article(s)
1
RNA polymerase I (Pol I) lobe-binding subunit Rpa12.2 promotes RNA cleavage and proofreading. J Biol Chem 2022;298:101862. [PMID: 35341765 PMCID: PMC9108883 DOI: 10.1016/j.jbc.2022.101862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/13/2022] [Accepted: 03/17/2022] [Indexed: 11/23/2022]  Open
2
Merkl PE, Schächner C, Pilsl M, Schwank K, Schmid C, Längst G, Milkereit P, Griesenbeck J, Tschochner H. Specialization of RNA Polymerase I in Comparison to Other Nuclear RNA Polymerases of Saccharomyces cerevisiae. Methods Mol Biol 2022;2533:63-70. [PMID: 35796982 PMCID: PMC9761553 DOI: 10.1007/978-1-0716-2501-9_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
3
Multisubunit DNA-Dependent RNA Polymerases from Vaccinia Virus and Other Nucleocytoplasmic Large-DNA Viruses: Impressions from the Age of Structure. Microbiol Mol Biol Rev 2017;81:81/3/e00010-17. [PMID: 28701329 DOI: 10.1128/mmbr.00010-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]  Open
4
Čabart P, Jin H, Li L, Kaplan CD. Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis. Transcription 2015;5:e28869. [PMID: 25764335 PMCID: PMC4574878 DOI: 10.4161/trns.28869] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
5
Ccr4-Not and TFIIS Function Cooperatively To Rescue Arrested RNA Polymerase II. Mol Cell Biol 2015;35:1915-25. [PMID: 25776559 DOI: 10.1128/mcb.00044-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/11/2015] [Indexed: 12/13/2022]  Open
6
Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms. Proc Natl Acad Sci U S A 2014;111:6642-7. [PMID: 24733897 DOI: 10.1073/pnas.1405181111] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
7
Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics. Proc Natl Acad Sci U S A 2014;111:3419-24. [PMID: 24550488 DOI: 10.1073/pnas.1401611111] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
8
Arginine-rich motifs are not required for hepatitis delta virus RNA binding activity of the hepatitis delta antigen. J Virol 2013;87:8665-74. [PMID: 23740973 DOI: 10.1128/jvi.00929-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
9
Palangat M, Larson DR. Complexity of RNA polymerase II elongation dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012;1819:667-72. [PMID: 22480952 DOI: 10.1016/j.bbagrm.2012.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 12/24/2022]
10
Luse DS, Studitsky VM. The mechanism of nucleosome traversal by RNA polymerase II: roles for template uncoiling and transcript elongation factors. RNA Biol 2011;8:581-5. [PMID: 21519186 DOI: 10.4161/rna.8.4.15389] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
11
Luse DS, Spangler LC, Újvári A. Efficient and rapid nucleosome traversal by RNA polymerase II depends on a combination of transcript elongation factors. J Biol Chem 2010;286:6040-8. [PMID: 21177855 DOI: 10.1074/jbc.m110.174722] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
12
Kireeva M, Kashlev M, Burton ZF. Translocation by multi-subunit RNA polymerases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010;1799:389-401. [PMID: 20097318 DOI: 10.1016/j.bbagrm.2010.01.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 01/14/2010] [Accepted: 01/14/2010] [Indexed: 11/30/2022]
13
Chen ZA, Jawhari A, Fischer L, Buchen C, Tahir S, Kamenski T, Rasmussen M, Lariviere L, Bukowski-Wills JC, Nilges M, Cramer P, Rappsilber J. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J 2010;29:717-26. [PMID: 20094031 PMCID: PMC2810376 DOI: 10.1038/emboj.2009.401] [Citation(s) in RCA: 316] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 12/10/2009] [Indexed: 11/09/2022]  Open
14
Sydow JF, Cramer P. RNA polymerase fidelity and transcriptional proofreading. Curr Opin Struct Biol 2009;19:732-9. [PMID: 19914059 DOI: 10.1016/j.sbi.2009.10.009] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 10/15/2009] [Accepted: 10/15/2009] [Indexed: 02/06/2023]
15
Hepatitis delta virus RNA replication. Viruses 2009;1:818-31. [PMID: 21994571 PMCID: PMC3185533 DOI: 10.3390/v1030818] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 11/03/2009] [Accepted: 11/03/2009] [Indexed: 12/12/2022]  Open
16
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: 9.8] [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]
17
Kireeva M, Nedialkov YA, Gong XQ, Zhang C, Xiong Y, Moon W, Burton ZF, Kashlev M. Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase. Methods 2009;48:333-45. [PMID: 19398005 DOI: 10.1016/j.ymeth.2009.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 04/05/2009] [Accepted: 04/06/2009] [Indexed: 11/16/2022]  Open
18
Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest ARR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS. Tiny RNAs associated with transcription start sites in animals. Nat Genet 2009;41:572-8. [PMID: 19377478 DOI: 10.1038/ng.312] [Citation(s) in RCA: 265] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 12/06/2008] [Indexed: 12/13/2022]
19
Ujvári A, Hsieh FK, Luse SW, Studitsky VM, Luse DS. Histone N-terminal tails interfere with nucleosome traversal by RNA polymerase II. J Biol Chem 2008;283:32236-43. [PMID: 18815126 DOI: 10.1074/jbc.m806636200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
20
Johnson RS, Strausbauch M, Cooper R, Register JK. Rapid kinetic analysis of transcription elongation by Escherichia coli RNA polymerase. J Mol Biol 2008;381:1106-13. [PMID: 18638485 DOI: 10.1016/j.jmb.2008.06.089] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 06/27/2008] [Accepted: 06/28/2008] [Indexed: 11/28/2022]
21
Yamaguchi Y, Mura T, Chanarat S, Okamoto S, Handa H. Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity. Genes Cells 2007;12:863-75. [PMID: 17584298 DOI: 10.1111/j.1365-2443.2007.01094.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
22
Burton ZF, Feig M, Gong XQ, Zhang C, Nedialkov YA, Xiong Y. NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases. Biochem Cell Biol 2005;83:486-96. [PMID: 16094452 DOI: 10.1139/o05-059] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
23
Palangat M, Renner DB, Price DH, Landick R. A negative elongation factor for human RNA polymerase II inhibits the anti-arrest transcript-cleavage factor TFIIS. Proc Natl Acad Sci U S A 2005;102:15036-41. [PMID: 16214896 PMCID: PMC1257689 DOI: 10.1073/pnas.0409405102] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Indexed: 01/22/2023]  Open
24
Gong XQ, Zhang C, Feig M, Burton ZF. Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol Cell 2005;18:461-70. [PMID: 15893729 DOI: 10.1016/j.molcel.2005.04.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 03/02/2005] [Accepted: 04/21/2005] [Indexed: 01/22/2023]
25
Kireeva ML, Hancock B, Cremona GH, Walter W, Studitsky VM, Kashlev M. Nature of the nucleosomal barrier to RNA polymerase II. Mol Cell 2005;18:97-108. [PMID: 15808512 DOI: 10.1016/j.molcel.2005.02.027] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Revised: 01/20/2005] [Accepted: 02/23/2005] [Indexed: 11/16/2022]
26
Langelier MF, Baali D, Trinh V, Greenblatt J, Archambault J, Coulombe B. The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II. Nucleic Acids Res 2005;33:2629-39. [PMID: 15886393 PMCID: PMC1092279 DOI: 10.1093/nar/gki570] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 04/21/2005] [Accepted: 04/21/2005] [Indexed: 11/13/2022]  Open
27
Zhang C, Zobeck KL, Burton ZF. Human RNA polymerase II elongation in slow motion: role of the TFIIF RAP74 alpha1 helix in nucleoside triphosphate-driven translocation. Mol Cell Biol 2005;25:3583-95. [PMID: 15831464 PMCID: PMC1084311 DOI: 10.1128/mcb.25.9.3583-3595.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 12/27/2004] [Accepted: 12/31/2004] [Indexed: 11/20/2022]  Open
28
Sims RJ, Belotserkovskaya R, Reinberg D. Elongation by RNA polymerase II: the short and long of it. Genes Dev 2004;18:2437-68. [PMID: 15489290 DOI: 10.1101/gad.1235904] [Citation(s) in RCA: 533] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
29
Zhang C, Burton ZF. Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism. J Mol Biol 2004;342:1085-99. [PMID: 15351637 DOI: 10.1016/j.jmb.2004.07.070] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2004] [Revised: 07/20/2004] [Accepted: 07/21/2004] [Indexed: 11/28/2022]
30
Ujvári A, Luse DS. Newly Initiated RNA encounters a factor involved in splicing immediately upon emerging from within RNA polymerase II. J Biol Chem 2004;279:49773-9. [PMID: 15377657 DOI: 10.1074/jbc.m409087200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
31
Park NJ, Tsao DC, Martinson HG. The two steps of poly(A)-dependent termination, pausing and release, can be uncoupled by truncation of the RNA polymerase II carboxyl-terminal repeat domain. Mol Cell Biol 2004;24:4092-103. [PMID: 15121832 PMCID: PMC400489 DOI: 10.1128/mcb.24.10.4092-4103.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
32
Gong XQ, Nedialkov YA, Burton ZF. Alpha-amanitin blocks translocation by human RNA polymerase II. J Biol Chem 2004;279:27422-7. [PMID: 15096519 DOI: 10.1074/jbc.m402163200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
33
Hawryluk PJ, Ujvári A, Luse DS. Characterization of a novel RNA polymerase II arrest site which lacks a weak 3' RNA-DNA hybrid. Nucleic Acids Res 2004;32:1904-16. [PMID: 15047857 PMCID: PMC390359 DOI: 10.1093/nar/gkh505] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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