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For: Ishii H, Kadonaga JT, Ren B. MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proc Natl Acad Sci U S A 2015;112:E3457-65. [PMID: 26080409 DOI: 10.1073/pnas.1424804112] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
Number Cited by Other Article(s)
1
Lu W, Liu Y, Li J, Huang S, Wen Z, Su C, Lu Z, Mo Z, Yu Z. Single-cell assay for transposase-accessible chromatin sequencing of human clear cell renal cell carcinoma. Sci Data 2025;12:334. [PMID: 40000710 PMCID: PMC11861977 DOI: 10.1038/s41597-025-04666-w] [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: 07/10/2024] [Accepted: 02/18/2025] [Indexed: 02/27/2025]  Open
2
Yang J, Yen K, Mahony S. Size-based expectation maximization for characterizing nucleosome positions and subtypes. Genome Res 2024;34:1334-1343. [PMID: 38886069 PMCID: PMC11529872 DOI: 10.1101/gr.279138.124] [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: 02/15/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024]
3
Wernig-Zorc S, Kugler F, Schmutterer L, Räß P, Hausmann C, Holzinger S, Längst G, Schwartz U. nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome. SCIENCE ADVANCES 2024;10:eadm9740. [PMID: 38959309 PMCID: PMC11221511 DOI: 10.1126/sciadv.adm9740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
4
Brandani GB, Gu C, Gopi S, Takada S. Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci. PNAS NEXUS 2024;3:pgae226. [PMID: 38881841 PMCID: PMC11179106 DOI: 10.1093/pnasnexus/pgae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024]
5
Yang J, Yen K, Mahony S. SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562727. [PMID: 37904910 PMCID: PMC10614873 DOI: 10.1101/2023.10.17.562727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
6
Zhang A, Li X, Zhao H, Jiang J, Zhang W. Genome-Wide Identification of Open Chromatin in Plants Using MH-Seq. Methods Mol Biol 2023;2594:29-43. [PMID: 36264486 DOI: 10.1007/978-1-0716-2815-7_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
7
A giant virus genome is densely packaged by stable nucleosomes within virions. Mol Cell 2022;82:4458-4470.e5. [PMID: 36370708 DOI: 10.1016/j.molcel.2022.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/09/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022]
8
Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022;13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022]  Open
9
Henikoff S, Ahmad K. In situ tools for chromatin structural epigenomics. Protein Sci 2022;31:e4458. [PMID: 36170035 PMCID: PMC9601787 DOI: 10.1002/pro.4458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
10
Talbert PB, Armache KJ, Henikoff S. Viral histones: pickpocket's prize or primordial progenitor? Epigenetics Chromatin 2022;15:21. [PMID: 35624484 PMCID: PMC9145170 DOI: 10.1186/s13072-022-00454-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022]  Open
11
Mapping nucleosome and chromatin architectures: A survey of computational methods. Comput Struct Biotechnol J 2022;20:3955-3962. [PMID: 35950186 PMCID: PMC9340519 DOI: 10.1016/j.csbj.2022.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 11/21/2022]  Open
12
Xu W, Wen Y, Liang Y, Xu Q, Wang X, Jin W, Chen X. A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility. Nat Protoc 2021;16:4084-4107. [PMID: 34282334 DOI: 10.1038/s41596-021-00583-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
13
Wilson SL, Wallingford M. Epigenetic regulation of reproduction in human and in animal models. Mol Hum Reprod 2021;27:6329199. [PMID: 34318322 DOI: 10.1093/molehr/gaab041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/07/2021] [Indexed: 12/24/2022]  Open
14
Chanou A, Hamperl S. Single-Molecule Techniques to Study Chromatin. Front Cell Dev Biol 2021;9:699771. [PMID: 34291054 PMCID: PMC8287188 DOI: 10.3389/fcell.2021.699771] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022]  Open
15
Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021;22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023]  Open
16
Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S. Chromatin accessibility profiling methods. NATURE REVIEWS. METHODS PRIMERS 2021;1:10. [PMID: 38410680 PMCID: PMC10895463 DOI: 10.1038/s43586-020-00008-9] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 02/06/2023]
17
Luse DS, Parida M, Spector BM, Nilson KA, Price DH. A unified view of the sequence and functional organization of the human RNA polymerase II promoter. Nucleic Acids Res 2020;48:7767-7785. [PMID: 32597978 PMCID: PMC7641323 DOI: 10.1093/nar/gkaa531] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/31/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]  Open
18
Oh S, Jo Y, Jung S, Yoon S, Yoo KH. From genome sequencing to the discovery of potential biomarkers in liver disease. BMB Rep 2020. [PMID: 32475383 PMCID: PMC7330805 DOI: 10.5483/bmbrep.2020.53.6.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
19
Hsieh THS, Cattoglio C, Slobodyanyuk E, Hansen AS, Rando OJ, Tjian R, Darzacq X. Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding. Mol Cell 2020;78:539-553.e8. [PMID: 32213323 PMCID: PMC7703524 DOI: 10.1016/j.molcel.2020.03.002] [Citation(s) in RCA: 373] [Impact Index Per Article: 74.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/28/2020] [Accepted: 03/02/2020] [Indexed: 01/31/2023]
20
Ramani V, Qiu R, Shendure J. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell Rep 2020;26:2465-2476.e4. [PMID: 30811994 PMCID: PMC6582983 DOI: 10.1016/j.celrep.2019.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/07/2018] [Accepted: 02/01/2019] [Indexed: 12/11/2022]  Open
21
Oruba A, Saccani S, van Essen D. Role of cell-type specific nucleosome positioning in inducible activation of mammalian promoters. Nat Commun 2020;11:1075. [PMID: 32103026 PMCID: PMC7044431 DOI: 10.1038/s41467-020-14950-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/10/2020] [Indexed: 12/18/2022]  Open
22
Epigenome Regulation by Dynamic Nucleosome Unwrapping. Trends Biochem Sci 2020;45:13-26. [PMID: 31630896 PMCID: PMC10168609 DOI: 10.1016/j.tibs.2019.09.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/09/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
23
Klein DC, Hainer SJ. Genomic methods in profiling DNA accessibility and factor localization. Chromosome Res 2019;28:69-85. [PMID: 31776829 PMCID: PMC7125251 DOI: 10.1007/s10577-019-09619-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 12/24/2022]
24
Chen FX, Smith ER, Shilatifard A. Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2019;19:464-478. [PMID: 29740129 DOI: 10.1038/s41580-018-0010-5] [Citation(s) in RCA: 288] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
25
Sun Y, Miao N, Sun T. Detect accessible chromatin using ATAC-sequencing, from principle to applications. Hereditas 2019;156:29. [PMID: 31427911 PMCID: PMC6696680 DOI: 10.1186/s41065-019-0105-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023]  Open
26
Luo D, Kato D, Nogami J, Ohkawa Y, Kurumizaka H, Kono H. MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast. Nucleic Acids Res 2019;46:7124-7137. [PMID: 29893974 PMCID: PMC6101533 DOI: 10.1093/nar/gky502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/30/2018] [Indexed: 01/06/2023]  Open
27
Wang Y, Wang A, Liu Z, Thurman AL, Powers LS, Zou M, Zhao Y, Hefel A, Li Y, Zabner J, Au KF. Single-molecule long-read sequencing reveals the chromatin basis of gene expression. Genome Res 2019;29:1329-1342. [PMID: 31201211 PMCID: PMC6673713 DOI: 10.1101/gr.251116.119] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/10/2019] [Indexed: 11/25/2022]
28
Starks RR, Biswas A, Jain A, Tuteja G. Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks. Epigenetics Chromatin 2019;12:16. [PMID: 30795793 PMCID: PMC6385419 DOI: 10.1186/s13072-019-0260-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/12/2019] [Indexed: 12/12/2022]  Open
29
Schwartz U, Németh A, Diermeier S, Exler JH, Hansch S, Maldonado R, Heizinger L, Merkl R, Längst G. Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin. Nucleic Acids Res 2019;47:1239-1254. [PMID: 30496478 PMCID: PMC6379673 DOI: 10.1093/nar/gky1203] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/17/2018] [Accepted: 11/22/2018] [Indexed: 12/22/2022]  Open
30
Nishimura M, Nozawa K, Kurumizaka H. Crystallographic analysis of the overlapping dinucleosome as a novel chromatin unit. Biophys Physicobiol 2019;15:251-254. [PMID: 30713825 PMCID: PMC6353640 DOI: 10.2142/biophysico.15.0_251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/18/2018] [Indexed: 12/01/2022]  Open
31
Brahma S, Henikoff S. RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast. Mol Cell 2018;73:238-249.e3. [PMID: 30554944 PMCID: PMC6475595 DOI: 10.1016/j.molcel.2018.10.046] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/04/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023]
32
Potdar P, Pinto P, D’Souza N, Joshi P, Malwade A, Sen S. A Novel Method to Generate MNase Ladders Reveal Rapid Chromatin Remodeling upon Gametogenesis and Mating in Chlamydomonas. Protist 2018;169:632-644. [DOI: 10.1016/j.protis.2018.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/22/2018] [Accepted: 06/27/2018] [Indexed: 02/06/2023]
33
Umeyama T, Ito T. DMS-seq for In Vivo Genome-Wide Mapping of Protein-DNA Interactions and Nucleosome Centers. ACTA ACUST UNITED AC 2018;123:e60. [PMID: 29927065 DOI: 10.1002/cpmb.60] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
34
Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq). Methods Mol Biol 2018;1689:83-101. [PMID: 29027167 DOI: 10.1007/978-1-4939-7380-4_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
35
Umeyama T, Ito T. DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers. Cell Rep 2018;21:289-300. [PMID: 28978481 DOI: 10.1016/j.celrep.2017.09.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/31/2017] [Accepted: 09/08/2017] [Indexed: 01/05/2023]  Open
36
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
37
Yu Z, Cowan JA. Metal complexes promoting catalytic cleavage of nucleic acids-biochemical tools and therapeutics. Curr Opin Chem Biol 2018;43:37-42. [PMID: 29153936 PMCID: PMC5847438 DOI: 10.1016/j.cbpa.2017.10.029] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/26/2017] [Accepted: 10/29/2017] [Indexed: 01/21/2023]
38
Fuse T, Katsumata K, Morohoshi K, Mukai Y, Ichikawa Y, Kurumizaka H, Yanagida A, Urano T, Kato H, Shimizu M. Parallel mapping with site-directed hydroxyl radicals and micrococcal nuclease reveals structural features of positioned nucleosomes in vivo. PLoS One 2017;12:e0186974. [PMID: 29073207 PMCID: PMC5658119 DOI: 10.1371/journal.pone.0186974] [Citation(s) in RCA: 5] [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: 06/14/2017] [Accepted: 10/11/2017] [Indexed: 12/17/2022]  Open
39
Kubik S, Bruzzone MJ, Albert B, Shore D. A Reply to "MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers," by Chereji et al. Mol Cell 2017;65:578-580. [PMID: 28157510 DOI: 10.1016/j.molcel.2017.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 11/25/2022]
40
MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers. Mol Cell 2017;65:565-577.e3. [PMID: 28157509 DOI: 10.1016/j.molcel.2016.12.009] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/15/2016] [Accepted: 12/13/2016] [Indexed: 11/24/2022]
41
Vo Ngoc L, Wang YL, Kassavetis GA, Kadonaga JT. The punctilious RNA polymerase II core promoter. Genes Dev 2017;31:1289-1301. [PMID: 28808065 PMCID: PMC5580651 DOI: 10.1101/gad.303149.117] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
42
Voong LN, Xi L, Wang JP, Wang X. Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping. Trends Genet 2017;33:495-507. [PMID: 28693826 DOI: 10.1016/j.tig.2017.05.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/10/2017] [Accepted: 05/30/2017] [Indexed: 12/30/2022]
43
Understanding nucleosome dynamics and their links to gene expression and DNA replication. Nat Rev Mol Cell Biol 2017;18:548-562. [PMID: 28537572 DOI: 10.1038/nrm.2017.47] [Citation(s) in RCA: 335] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
44
Mueller B, Mieczkowski J, Kundu S, Wang P, Sadreyev R, Tolstorukov MY, Kingston RE. Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction. Genes Dev 2017;31:451-462. [PMID: 28356342 PMCID: PMC5393060 DOI: 10.1101/gad.293118.116] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022]
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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]
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Vainshtein Y, Rippe K, Teif VB. NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data. BMC Genomics 2017;18:158. [PMID: 28196481 PMCID: PMC5309995 DOI: 10.1186/s12864-017-3580-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/10/2017] [Indexed: 12/21/2022]  Open
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Voong LN, Xi L, Sebeson AC, Xiong B, Wang JP, Wang X. Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping. Cell 2016;167:1555-1570.e15. [PMID: 27889238 DOI: 10.1016/j.cell.2016.10.049] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/05/2016] [Accepted: 10/27/2016] [Indexed: 12/21/2022]
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Maksimov DA, Laktionov PP, Belyakin SN. Data analysis algorithm for DamID-seq profiling of chromatin proteins in Drosophila melanogaster. Chromosome Res 2016;24:481-494. [DOI: 10.1007/s10577-016-9538-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 11/29/2022]
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In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences. Sci Rep 2016;6:32476. [PMID: 27582178 PMCID: PMC5007594 DOI: 10.1038/srep32476] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/08/2016] [Indexed: 01/06/2023]  Open
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MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat Commun 2016;7:11485. [PMID: 27151365 PMCID: PMC4859066 DOI: 10.1038/ncomms11485] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/31/2016] [Indexed: 01/01/2023]  Open
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