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For: Lorch Y, Davis B, Kornberg RD. Chromatin remodeling by DNA bending, not twisting. Proc Natl Acad Sci U S A 2005;102:1329-32. [PMID: 15677336 PMCID: PMC546017 DOI: 10.1073/pnas.0409413102] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
Number Cited by Other Article(s)
1
Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nat Commun 2024;15:3663. [PMID: 38688943 PMCID: PMC11061278 DOI: 10.1038/s41467-024-47830-3] [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: 02/21/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]  Open
2
Khatua P, Tang PK, Moulick AG, Patel R, Manandhar A, Loverde SM. Sequence Dependence in Nucleosome Dynamics. J Phys Chem B 2024;128:3090-3101. [PMID: 38530903 PMCID: PMC11181342 DOI: 10.1021/acs.jpcb.3c07363] [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] [Indexed: 03/28/2024]
3
Lorch Y, Kornberg RD, Maier-Davis B. Role of the histone tails in histone octamer transfer. Nucleic Acids Res 2023;51:3671-3678. [PMID: 36772826 PMCID: PMC10164550 DOI: 10.1093/nar/gkad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 02/12/2023]  Open
4
Disruption of nucleosomes by DNA groove binders of clinical significance and implications for chromatin remodeling. Proc Natl Acad Sci U S A 2023;120:e2216611120. [PMID: 36574674 PMCID: PMC9910476 DOI: 10.1073/pnas.2216611120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
5
Nodelman IM, Bowman GD. Biophysics of Chromatin Remodeling. Annu Rev Biophys 2021;50:73-93. [PMID: 33395550 DOI: 10.1146/annurev-biophys-082520-080201] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
6
Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R. DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature 2020;587:291-296. [PMID: 33087930 PMCID: PMC7666076 DOI: 10.1038/s41586-020-2843-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 09/17/2020] [Indexed: 12/17/2022]
7
Markert J, Luger K. Nucleosomes Meet Their Remodeler Match. Trends Biochem Sci 2020;46:41-50. [PMID: 32917506 DOI: 10.1016/j.tibs.2020.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
8
Lequieu J, Córdoba A, Moller J, de Pablo JJ. 1CPN: A coarse-grained multi-scale model of chromatin. J Chem Phys 2019;150:215102. [PMID: 31176328 DOI: 10.1063/1.5092976] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
9
Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling. Nat Commun 2019;10:1720. [PMID: 30979890 PMCID: PMC6461674 DOI: 10.1038/s41467-019-09657-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/20/2019] [Indexed: 11/11/2022]  Open
10
Guo AZ, Lequieu J, de Pablo JJ. Extracting collective motions underlying nucleosome dynamics via nonlinear manifold learning. J Chem Phys 2019;150:054902. [PMID: 30736679 DOI: 10.1063/1.5063851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
11
Lorch Y, Maier-Davis B, Kornberg RD. Histone Acetylation Inhibits RSC and Stabilizes the +1 Nucleosome. Mol Cell 2018;72:594-600.e2. [PMID: 30401433 PMCID: PMC6290470 DOI: 10.1016/j.molcel.2018.09.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 12/12/2022]
12
Chromatin-remodeling for transcription. Q Rev Biophys 2018;50:e5. [PMID: 29233217 DOI: 10.1017/s003358351700004x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
13
Lequieu J, Schwartz DC, de Pablo JJ. In silico evidence for sequence-dependent nucleosome sliding. Proc Natl Acad Sci U S A 2017;114:E9197-E9205. [PMID: 29078285 PMCID: PMC5676884 DOI: 10.1073/pnas.1705685114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
14
INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers. Nat Commun 2017;8:15616. [PMID: 28604691 PMCID: PMC5472786 DOI: 10.1038/ncomms15616] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 04/12/2017] [Indexed: 12/27/2022]  Open
15
Volokh OI, Derkacheva NI, Studitsky VM, Sokolova OS. Structural studies of chromatin remodeling factors. Mol Biol 2016. [DOI: 10.1134/s0026893316060212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
16
Skulte KA, Phan L, Clark SJ, Taberlay PC. Chromatin remodeler mutations in human cancers: epigenetic implications. Epigenomics 2015;6:397-414. [PMID: 25333849 DOI: 10.2217/epi.14.37] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
17
Lorch Y, Maier-Davis B, Kornberg RD. Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions. Genes Dev 2015;28:2492-7. [PMID: 25403179 PMCID: PMC4233242 DOI: 10.1101/gad.250704.114] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
18
Bartholomew B. Regulating the chromatin landscape: structural and mechanistic perspectives. Annu Rev Biochem 2014;83:671-96. [PMID: 24606138 DOI: 10.1146/annurev-biochem-051810-093157] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
19
Mueller-Planitz F, Klinker H, Becker PB. Nucleosome sliding mechanisms: new twists in a looped history. Nat Struct Mol Biol 2013;20:1026-32. [PMID: 24008565 DOI: 10.1038/nsmb.2648] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 07/12/2013] [Indexed: 01/11/2023]
20
Deindl S, Hwang WL, Hota SK, Blosser TR, Prasad P, Bartholomew B, Zhuang X. ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps. Cell 2013;152:442-52. [PMID: 23374341 DOI: 10.1016/j.cell.2012.12.040] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 10/16/2012] [Accepted: 12/17/2012] [Indexed: 12/27/2022]
21
Viswanathan R, Auble DT. One small step for Mot1; one giant leap for other Swi2/Snf2 enzymes? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011;1809:488-96. [PMID: 21658482 DOI: 10.1016/j.bbagrm.2011.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/14/2011] [Accepted: 05/20/2011] [Indexed: 12/13/2022]
22
Diversity of operation in ATP-dependent chromatin remodelers. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011;1809:476-87. [PMID: 21616185 DOI: 10.1016/j.bbagrm.2011.05.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/28/2011] [Accepted: 05/09/2011] [Indexed: 12/20/2022]
23
Mechanism of chromatin remodeling. Proc Natl Acad Sci U S A 2010;107:3458-62. [PMID: 20142505 DOI: 10.1073/pnas.1000398107] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
24
Bowman GD. Mechanisms of ATP-dependent nucleosome sliding. Curr Opin Struct Biol 2010;20:73-81. [PMID: 20060707 DOI: 10.1016/j.sbi.2009.12.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2009] [Revised: 12/07/2009] [Accepted: 12/08/2009] [Indexed: 10/20/2022]
25
Stojanova A, Penn LZ. The role of INI1/hSNF5 in gene regulation and cancer. Biochem Cell Biol 2009;87:163-77. [PMID: 19234532 DOI: 10.1139/o08-113] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
26
Structure of a RSC-nucleosome complex and insights into chromatin remodeling. Nat Struct Mol Biol 2008;15:1272-7. [PMID: 19029894 DOI: 10.1038/nsmb.1524] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 10/31/2008] [Indexed: 12/21/2022]
27
Cairns BR. Chromatin remodeling: insights and intrigue from single-molecule studies. Nat Struct Mol Biol 2008;14:989-96. [PMID: 17984961 DOI: 10.1038/nsmb1333] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
28
Choudhary P, Varga-Weisz P. ATP-dependent chromatin remodelling: action and reaction. Subcell Biochem 2007;41:29-43. [PMID: 17484122 DOI: 10.1007/1-4020-5466-1_2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
29
Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, Cairns BR, Peterson CL, Bustamante C. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell 2007;24:559-68. [PMID: 17188033 PMCID: PMC9034902 DOI: 10.1016/j.molcel.2006.10.025] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 09/26/2006] [Accepted: 10/23/2006] [Indexed: 10/23/2022]
30
Saha A, Wittmeyer J, Cairns BR. Chromatin remodelling: the industrial revolution of DNA around histones. Nat Rev Mol Cell Biol 2006;7:437-47. [PMID: 16723979 DOI: 10.1038/nrm1945] [Citation(s) in RCA: 400] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
31
Li W, Dou SX, Xie P, Wang PY. Brownian dynamics simulation of directional sliding of histone octamers caused by DNA bending. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006;73:051909. [PMID: 16802969 DOI: 10.1103/physreve.73.051909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Indexed: 05/10/2023]
32
Saha A, Wittmeyer J, Cairns BR. Mechanisms for nucleosome movement by ATP-dependent chromatin remodeling complexes. Results Probl Cell Differ 2006;41:127-48. [PMID: 16909894 DOI: 10.1007/400_005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
33
Zofall M, Persinger J, Kassabov SR, Bartholomew B. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat Struct Mol Biol 2006;13:339-46. [PMID: 16518397 DOI: 10.1038/nsmb1071] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Accepted: 01/25/2006] [Indexed: 11/09/2022]
34
Lorch Y, Maier-Davis B, Kornberg RD. Chromatin remodeling by nucleosome disassembly in vitro. Proc Natl Acad Sci U S A 2006;103:3090-3. [PMID: 16492771 PMCID: PMC1413907 DOI: 10.1073/pnas.0511050103] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
35
Becker PB. Nucleosome remodelers on track. Nat Struct Mol Biol 2005;12:732-3. [PMID: 16142222 DOI: 10.1038/nsmb0905-732] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
36
Saha A, Wittmeyer J, Cairns BR. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat Struct Mol Biol 2005;12:747-55. [PMID: 16086025 DOI: 10.1038/nsmb973] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Accepted: 07/01/2005] [Indexed: 11/08/2022]
37
Strohner R, Wachsmuth M, Dachauer K, Mazurkiewicz J, Hochstatter J, Rippe K, Längst G. A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling. Nat Struct Mol Biol 2005;12:683-90. [PMID: 16025127 DOI: 10.1038/nsmb966] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 06/23/2005] [Indexed: 11/10/2022]
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