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For: Kang W, Ha KS, Uhm H, Park K, Lee JY, Hohng S, Kang C. Transcription reinitiation by recycling RNA polymerase that diffuses on DNA after releasing terminated RNA. Nat Commun 2020;11:450. [PMID: 31974350 PMCID: PMC6978380 DOI: 10.1038/s41467-019-14200-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/10/2019] [Indexed: 11/24/2022]  Open
Number Cited by Other Article(s)
1
Xu W, Collette D, Qian J, Finzi L, Dunlap D. Insights on the effect of macromolecular crowding on transcription and its regulation. QRB DISCOVERY 2025;6:e16. [PMID: 40395559 PMCID: PMC12088913 DOI: 10.1017/qrd.2025.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 03/10/2025] [Accepted: 03/15/2025] [Indexed: 05/22/2025]  Open
2
Brewer JJ, Inlow K, Mooney RA, Bosch B, Olinares PDB, Marcelino LP, Chait BT, Landick R, Gelles J, Campbell EA, Darst SA. RapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation. Nat Struct Mol Biol 2025;32:639-649. [PMID: 39779919 PMCID: PMC11996608 DOI: 10.1038/s41594-024-01447-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 11/07/2024] [Indexed: 01/11/2025]
3
Qian J, Wang B, Artsimovitch I, Dunlap D, Finzi L. Force and the α-C-terminal domains bias RNA polymerase recycling. Nat Commun 2024;15:7520. [PMID: 39214958 PMCID: PMC11364550 DOI: 10.1038/s41467-024-51603-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 08/13/2024] [Indexed: 09/04/2024]  Open
4
Song E, Han S, Uhm H, Kang C, Hohng S. Single-mode termination of phage transcriptions, disclosing bacterial adaptation for facilitated reinitiations. Nucleic Acids Res 2024;52:9092-9102. [PMID: 39011892 PMCID: PMC11347151 DOI: 10.1093/nar/gkae620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/24/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024]  Open
5
Xiong Y, Han W, Xu C, Shi J, Wang L, Jin T, Jia Q, Lu Y, Hu S, Dou SX, Lin W, Strick TR, Wang S, Li M. Single-molecule reconstruction of eukaryotic factor-dependent transcription termination. Nat Commun 2024;15:5113. [PMID: 38879529 PMCID: PMC11180205 DOI: 10.1038/s41467-024-49527-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/09/2024] [Indexed: 06/19/2024]  Open
6
Song E, Han S, Hohng S, Kang C. Compatibility of termination mechanisms in bacterial transcription with inference on eukaryotic models. Biochem Soc Trans 2024;52:887-897. [PMID: 38533838 DOI: 10.1042/bst20231229] [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: 01/19/2024] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
7
Giraud G, El Achi K, Zoulim F, Testoni B. Co-Transcriptional Regulation of HBV Replication: RNA Quality Also Matters. Viruses 2024;16:615. [PMID: 38675956 PMCID: PMC11053573 DOI: 10.3390/v16040615] [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: 03/25/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]  Open
8
Wang L. RNA polymerase collisions and their role in transcription. Transcription 2024;15:38-47. [PMID: 38357902 PMCID: PMC11093029 DOI: 10.1080/21541264.2024.2316972] [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: 11/06/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]  Open
9
Lim G, Hwang S, Yu K, Kang JY, Kang C, Hohng S. Translocating RNA polymerase generates R-loops at DNA double-strand breaks without any additional factors. Nucleic Acids Res 2023;51:9838-9848. [PMID: 37638763 PMCID: PMC10570047 DOI: 10.1093/nar/gkad689] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023]  Open
10
Yao X, Zhao Y, Hou W, Huang K, Yan M, Tu R, Goto T, Dai H. Multifunctional magnetocaloric bone cement with a time-varying alkaline microenvironment for sequential bacterial inhibition, angiogenesis and osteogenesis. J Mater Chem B 2023;11:9532-9544. [PMID: 37750817 DOI: 10.1039/d3tb01533e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
11
Tenenbaum D, Inlow K, Friedman LJ, Cai A, Gelles J, Kondev J. RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons. Proc Natl Acad Sci U S A 2023;120:e2301402120. [PMID: 37459525 PMCID: PMC10372574 DOI: 10.1073/pnas.2301402120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/19/2023] [Indexed: 07/20/2023]  Open
12
Inlow K, Tenenbaum D, Friedman LJ, Kondev J, Gelles J. Recycling of bacterial RNA polymerase by the Swi2/Snf2 ATPase RapA. Proc Natl Acad Sci U S A 2023;120:e2303849120. [PMID: 37406096 PMCID: PMC10334767 DOI: 10.1073/pnas.2303849120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023]  Open
13
Ni X, Liu Z, Guo J, Zhang G. Development of Terminator-Promoter Bifunctional Elements for Application in Saccharomyces cerevisiae Pathway Engineering. Int J Mol Sci 2023;24:9870. [PMID: 37373018 DOI: 10.3390/ijms24129870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023]  Open
14
Wang L, Watters JW, Ju X, Lu G, Liu S. Head-on and co-directional RNA polymerase collisions orchestrate bidirectional transcription termination. Mol Cell 2023;83:1153-1164.e4. [PMID: 36917983 PMCID: PMC10081963 DOI: 10.1016/j.molcel.2023.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/03/2023] [Accepted: 02/15/2023] [Indexed: 03/14/2023]
15
Inlow K, Tenenbaum D, Friedman LJ, Kondev J, Gelles J. Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533849. [PMID: 36993374 PMCID: PMC10055430 DOI: 10.1101/2023.03.22.533849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
16
Tenenbaum D, Inlow K, Friedman L, Cai A, Gelles J, Kondev J. RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.528045. [PMID: 36798213 PMCID: PMC9934669 DOI: 10.1101/2023.02.10.528045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
17
Song E, Hwang S, Munasingha PR, Seo YS, Kang J, Kang C, Hohng S. Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination. Nucleic Acids Res 2023;51:2778-2789. [PMID: 36762473 PMCID: PMC10085680 DOI: 10.1093/nar/gkad051] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/30/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023]  Open
18
You L, Omollo EO, Yu C, Mooney RA, Shi J, Shen L, Wu X, Wen A, He D, Zeng Y, Feng Y, Landick R, Zhang Y. Structural basis for intrinsic transcription termination. Nature 2023;613:783-789. [PMID: 36631609 PMCID: PMC10091898 DOI: 10.1038/s41586-022-05604-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/25/2022] [Indexed: 01/13/2023]
19
Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-André C, Weixlbaumer A. Structural insights into RNA-mediated transcription regulation in bacteria. Mol Cell 2022;82:3885-3900.e10. [DOI: 10.1016/j.molcel.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/07/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
20
Du J, Dartawan R, Rice W, Gao F, Zhou JH, Sheng J. Fluorescent Platforms for RNA Chemical Biology Research. Genes (Basel) 2022;13:1348. [PMID: 36011259 PMCID: PMC9407474 DOI: 10.3390/genes13081348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022]  Open
21
Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation. Proc Natl Acad Sci U S A 2021;118:2109026118. [PMID: 34782462 DOI: 10.1073/pnas.2109026118] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 11/18/2022]  Open
22
Qayyum MZ, Molodtsov V, Renda A, Murakami KS. Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli. J Biol Chem 2021;297:101404. [PMID: 34774797 PMCID: PMC8666675 DOI: 10.1016/j.jbc.2021.101404] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 01/27/2023]  Open
23
Wiedermannová J, Krásný L. β-CASP proteins removing RNA polymerase from DNA: when a torpedo is needed to shoot a sitting duck. Nucleic Acids Res 2021;49:10221-10234. [PMID: 34551438 PMCID: PMC8501993 DOI: 10.1093/nar/gkab803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022]  Open
24
Yi X, Khey J, Kazlauskas RJ, Travisano M. Plasmid hypermutation using a targeted artificial DNA replisome. SCIENCE ADVANCES 2021;7:7/29/eabg8712. [PMID: 34272238 PMCID: PMC8284885 DOI: 10.1126/sciadv.abg8712] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
25
The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation. J Bacteriol 2021;203:JB.00512-20. [PMID: 33139481 DOI: 10.1128/jb.00512-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
26
Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription. Int J Mol Sci 2021;22:ijms22052398. [PMID: 33673662 PMCID: PMC7957599 DOI: 10.3390/ijms22052398] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/08/2021] [Accepted: 02/24/2021] [Indexed: 11/17/2022]  Open
27
Pei HH, Hilal T, Chen ZA, Huang YH, Gao Y, Said N, Loll B, Rappsilber J, Belogurov GA, Artsimovitch I, Wahl MC. The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling. Nat Commun 2020;11:6418. [PMID: 33339827 PMCID: PMC7749165 DOI: 10.1038/s41467-020-20159-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022]  Open
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