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For: Chereji RV, Morozov AV. Ubiquitous nucleosome crowding in the yeast genome. Proc Natl Acad Sci U S A 2014;111:5236-41. [PMID: 24706846 DOI: 10.1073/pnas.1321001111] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
Number Cited by Other Article(s)
1
Hungyo K, Audit B, Vaillant C, Morozov AV. Thermodynamics of nucleosome breathing and positioning. J Chem Phys 2025;162:025101. [PMID: 39774893 DOI: 10.1063/5.0245457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2024] [Accepted: 12/20/2024] [Indexed: 01/11/2025]  Open
2
Are extraordinary nucleosome structures more ordinary than we thought? Chromosoma 2023:10.1007/s00412-023-00791-w. [PMID: 36917245 DOI: 10.1007/s00412-023-00791-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/16/2023]
3
Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast. BIOLOGY 2020;9:biology9080190. [PMID: 32722483 PMCID: PMC7466152 DOI: 10.3390/biology9080190] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
4
Chereji RV, Bryson TD, Henikoff S. Quantitative MNase-seq accurately maps nucleosome occupancy levels. Genome Biol 2019;20:198. [PMID: 31519205 PMCID: PMC6743174 DOI: 10.1186/s13059-019-1815-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 09/04/2019] [Indexed: 12/15/2022]  Open
5
Chereji RV, Eriksson PR, Ocampo J, Prajapati HK, Clark DJ. Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation. Genome Res 2019;29:1985-1995. [PMID: 31511305 PMCID: PMC6886500 DOI: 10.1101/gr.249326.119] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/26/2019] [Indexed: 02/06/2023]
6
Nucleosome positions alone can be used to predict domains in yeast chromosomes. Proc Natl Acad Sci U S A 2019;116:17307-17315. [PMID: 31416914 PMCID: PMC6717315 DOI: 10.1073/pnas.1817829116] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
7
Fierz B, Poirier MG. Biophysics of Chromatin Dynamics. Annu Rev Biophys 2019;48:321-345. [DOI: 10.1146/annurev-biophys-070317-032847] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
8
Winogradoff D, Aksimentiev A. Molecular Mechanism of Spontaneous Nucleosome Unraveling. J Mol Biol 2019;431:323-335. [PMID: 30468737 PMCID: PMC6331254 DOI: 10.1016/j.jmb.2018.11.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/26/2018] [Accepted: 11/12/2018] [Indexed: 11/18/2022]
9
Intracellular nucleosomes constrain a DNA linking number difference of -1.26 that reconciles the Lk paradox. Nat Commun 2018;9:3989. [PMID: 30266901 PMCID: PMC6162219 DOI: 10.1038/s41467-018-06547-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/11/2018] [Indexed: 02/07/2023]  Open
10
Jin H, Finnegan AI, Song JS. A unified computational framework for modeling genome-wide nucleosome landscape. Phys Biol 2018;15:066011. [PMID: 30113318 PMCID: PMC6170202 DOI: 10.1088/1478-3975/aadad2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
11
Bameta T, Das D, Padinhateeri R. Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer. Nucleic Acids Res 2018;46:4991-5000. [PMID: 29850895 PMCID: PMC6007630 DOI: 10.1093/nar/gky207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/09/2018] [Indexed: 01/09/2023]  Open
12
Chereji RV, Clark DJ. Major Determinants of Nucleosome Positioning. Biophys J 2018;114:2279-2289. [PMID: 29628211 DOI: 10.1016/j.bpj.2018.03.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 12/21/2022]  Open
13
Chereji RV, Ramachandran S, Bryson TD, Henikoff S. Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biol 2018;19:19. [PMID: 29426353 PMCID: PMC5807854 DOI: 10.1186/s13059-018-1398-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 01/24/2018] [Indexed: 11/10/2022]  Open
14
Gutiérrez G, Millán-Zambrano G, Medina DA, Jordán-Pla A, Pérez-Ortín JE, Peñate X, Chávez S. Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning. Epigenetics Chromatin 2017;10:58. [PMID: 29212533 PMCID: PMC5719526 DOI: 10.1186/s13072-017-0165-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022]  Open
15
Culkin J, de Bruin L, Tompitak M, Phillips R, Schiessel H. The role of DNA sequence in nucleosome breathing. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017;40:106. [PMID: 29185124 PMCID: PMC7001874 DOI: 10.1140/epje/i2017-11596-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/14/2017] [Indexed: 05/05/2023]
16
Meng H, Li H, Zheng Y, Yang Z, Jia Y, Bo S. Evolutionary analysis of nucleosome positioning sequences based on New Symmetric Relative Entropy. Genomics 2017;110:154-161. [PMID: 28917635 DOI: 10.1016/j.ygeno.2017.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/06/2017] [Accepted: 09/12/2017] [Indexed: 10/18/2022]
17
Kubik S, Bruzzone MJ, Shore D. Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler. Bioessays 2017;39. [PMID: 28345796 DOI: 10.1002/bies.201600237] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
18
Zhang B, Zheng W, Papoian GA, Wolynes PG. Exploring the Free Energy Landscape of Nucleosomes. J Am Chem Soc 2016;138:8126-33. [DOI: 10.1021/jacs.6b02893] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
19
Eslami-Mossallam B, Schiessel H, van Noort J. Nucleosome dynamics: Sequence matters. Adv Colloid Interface Sci 2016;232:101-113. [PMID: 26896338 DOI: 10.1016/j.cis.2016.01.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 02/06/2023]
20
Chereji RV, Kan TW, Grudniewska MK, Romashchenko AV, Berezikov E, Zhimulev IF, Guryev V, Morozov AV, Moshkin YM. Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster. Nucleic Acids Res 2016;44:1036-51. [PMID: 26429969 PMCID: PMC4756854 DOI: 10.1093/nar/gkv978] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/27/2015] [Accepted: 09/16/2015] [Indexed: 01/09/2023]  Open
21
Ocampo J, Chereji RV, Eriksson PR, Clark DJ. The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo. Nucleic Acids Res 2016;44:4625-35. [PMID: 26861626 PMCID: PMC4889916 DOI: 10.1093/nar/gkw068] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/28/2016] [Indexed: 12/17/2022]  Open
22
Teif VB. Nucleosome positioning: resources and tools online. Brief Bioinform 2015;17:745-57. [PMID: 26411474 DOI: 10.1093/bib/bbv086] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 01/08/2023]  Open
23
Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Genome Res 2015;25:1757-70. [PMID: 26314830 PMCID: PMC4617971 DOI: 10.1101/gr.192294.115] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/21/2015] [Indexed: 01/12/2023]
24
Sheinman M, Chung HR. Conditions for positioning of nucleosomes on DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015;92:022704. [PMID: 26382429 DOI: 10.1103/physreve.92.022704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Indexed: 06/05/2023]
25
Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015;115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 353] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
26
Teif VB, Kepper N, Yserentant K, Wedemann G, Rippe K. Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015;27:064110. [PMID: 25563825 DOI: 10.1088/0953-8984/27/6/064110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
27
Chereji RV, Morozov AV. Functional roles of nucleosome stability and dynamics. Brief Funct Genomics 2015;14:50-60. [PMID: 25275099 PMCID: PMC4366587 DOI: 10.1093/bfgp/elu038] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
28
Nucleosome positioning in yeasts: methods, maps, and mechanisms. Chromosoma 2014;124:131-51. [PMID: 25529773 DOI: 10.1007/s00412-014-0501-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 01/23/2023]
29
Osberg B, Nuebler J, Korber P, Gerland U. Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays. Nucleic Acids Res 2014;42:13633-45. [PMID: 25428353 PMCID: PMC4267636 DOI: 10.1093/nar/gku1190] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 11/13/2022]  Open
30
Beshnova DA, Cherstvy AG, Vainshtein Y, Teif VB. Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions. PLoS Comput Biol 2014;10:e1003698. [PMID: 24992723 PMCID: PMC4081033 DOI: 10.1371/journal.pcbi.1003698] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/16/2014] [Indexed: 12/12/2022]  Open
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