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For: Baek S, Sung MH, Hager GL. Quantitative analysis of genome-wide chromatin remodeling. Methods Mol Biol 2012;833:433-41. [PMID: 22183609 PMCID: PMC6391053 DOI: 10.1007/978-1-61779-477-3_26] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Number Cited by Other Article(s)
1
Amin R, Shukla A, Zhu JJ, Kim S, Wang P, Tian SZ, Tran AD, Paul D, Cappell SD, Burkett S, Liu H, Lee MP, Kruhlak MJ, Dwyer JE, Simpson RM, Hager GL, Ruan Y, Hunter KW. Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response. Nat Commun 2021;12:7216. [PMID: 34903738 PMCID: PMC8669001 DOI: 10.1038/s41467-021-27451-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/16/2021] [Indexed: 12/26/2022]  Open
2
Liu Y, Fu L, Kaufmann K, Chen D, Chen M. A practical guide for DNase-seq data analysis: from data management to common applications. Brief Bioinform 2020;20:1865-1877. [PMID: 30010713 DOI: 10.1093/bib/bby057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/06/2018] [Accepted: 06/10/2018] [Indexed: 01/01/2023]  Open
3
Fitz J, Neumann T, Steininger M, Wiedemann EM, Garcia AC, Athanasiadis A, Schoeberl UE, Pavri R. Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction. Nat Genet 2020;52:505-515. [PMID: 32251373 DOI: 10.1038/s41588-020-0605-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/28/2020] [Indexed: 12/19/2022]
4
Chang P, Gohain M, Yen MR, Chen PY. Computational Methods for Assessing Chromatin Hierarchy. Comput Struct Biotechnol J 2018;16:43-53. [PMID: 29686798 PMCID: PMC5910504 DOI: 10.1016/j.csbj.2018.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/29/2018] [Accepted: 02/11/2018] [Indexed: 12/27/2022]  Open
5
Portuguez AS, Schwartz M, Siersbaek R, Nielsen R, Sung MH, Mandrup S, Kaplan T, Hakim O. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis. FEBS J 2017;284:3230-3244. [PMID: 28755519 PMCID: PMC5626622 DOI: 10.1111/febs.14183] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/24/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022]
6
Gibson MD, Brehove M, Luo Y, North J, Poirier MG. Methods for Investigating DNA Accessibility with Single Nucleosomes. Methods Enzymol 2017;581:379-415. [PMID: 27793287 DOI: 10.1016/bs.mie.2016.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
7
Anti-Inflammatory Chromatinscape Suggests Alternative Mechanisms of Glucocorticoid Receptor Action. Immunity 2017;47:298-309.e5. [PMID: 28801231 DOI: 10.1016/j.immuni.2017.07.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 03/14/2017] [Accepted: 07/19/2017] [Indexed: 11/21/2022]
8
Pooley JR, Flynn BP, Grøntved L, Baek S, Guertin MJ, Kershaw YM, Birnie MT, Pellatt A, Rivers CA, Schiltz RL, Hager GL, Lightman SL, Conway-Campbell BL. Genome-Wide Identification of Basic Helix-Loop-Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus. Endocrinology 2017;158:1486-1501. [PMID: 28200020 PMCID: PMC5460825 DOI: 10.1210/en.2016-1929] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/03/2017] [Indexed: 12/14/2022]
9
Baskin E, Farouni R, Mathé EA. ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data. Bioinformatics 2017;33:740-742. [PMID: 28011773 PMCID: PMC5408819 DOI: 10.1093/bioinformatics/btw688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/26/2016] [Indexed: 11/13/2022]  Open
10
Goldstein I, Baek S, Presman DM, Paakinaho V, Swinstead EE, Hager GL. Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response. Genome Res 2016;27:427-439. [PMID: 28031249 PMCID: PMC5340970 DOI: 10.1101/gr.212175.116] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/21/2016] [Indexed: 02/03/2023]
11
Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome. PLoS One 2016;11:e0165581. [PMID: 27798693 PMCID: PMC5087912 DOI: 10.1371/journal.pone.0165581] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/16/2016] [Indexed: 01/06/2023]  Open
12
Genome-wide footprinting: ready for prime time? Nat Methods 2016;13:222-228. [PMID: 26914206 DOI: 10.1038/nmeth.3766] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/31/2015] [Indexed: 01/16/2023]
13
Thompson B, Varticovski L, Baek S, Hager GL. Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation. PLoS One 2016;11:e0148619. [PMID: 26890492 PMCID: PMC4759368 DOI: 10.1371/journal.pone.0148619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 01/20/2016] [Indexed: 12/17/2022]  Open
14
Baek S, Sung MH. Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes. Methods Mol Biol 2016;1418:225-40. [PMID: 27008018 DOI: 10.1007/978-1-4939-3578-9_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
15
Wang C, Lv Y, Wang B, Yin C, Lin Y, Pan L. Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale. Nucleic Acids Res 2015;43:4429-46. [PMID: 25883143 PMCID: PMC4482085 DOI: 10.1093/nar/gkv334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 03/31/2015] [Indexed: 01/23/2023]  Open
16
Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling. Nat Commun 2015;6:7048. [PMID: 25916672 DOI: 10.1038/ncomms8048] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/26/2015] [Indexed: 02/03/2023]  Open
17
Tsompana M, Buck MJ. Chromatin accessibility: a window into the genome. Epigenetics Chromatin 2014;7:33. [PMID: 25473421 PMCID: PMC4253006 DOI: 10.1186/1756-8935-7-33] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/05/2014] [Indexed: 01/09/2023]  Open
18
Hsiung CCS, Morrissey CS, Udugama M, Frank CL, Keller CA, Baek S, Giardine B, Crawford GE, Sung MH, Hardison RC, Blobel GA. Genome accessibility is widely preserved and locally modulated during mitosis. Genome Res 2014;25:213-25. [PMID: 25373146 PMCID: PMC4315295 DOI: 10.1101/gr.180646.114] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
19
Koohy H, Down TA, Spivakov M, Hubbard T. A comparison of peak callers used for DNase-Seq data. PLoS One 2014;9:e96303. [PMID: 24810143 PMCID: PMC4014496 DOI: 10.1371/journal.pone.0096303] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 04/06/2014] [Indexed: 11/19/2022]  Open
20
Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 2014;155:1507-20. [PMID: 24360274 DOI: 10.1016/j.cell.2013.11.039] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/01/2013] [Accepted: 11/25/2013] [Indexed: 12/31/2022]
21
Morris SA, Baek S, Sung MH, John S, Wiench M, Johnson TA, Schiltz RL, Hager GL. Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions. Nat Struct Mol Biol 2013;21:73-81. [PMID: 24317492 PMCID: PMC3947387 DOI: 10.1038/nsmb.2718] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 10/17/2013] [Indexed: 12/24/2022]
22
Miranda TB, Voss TC, Sung MH, Baek S, John S, Hawkins M, Grøntved L, Schiltz RL, Hager GL. Reprogramming the chromatin landscape: interplay of the estrogen and glucocorticoid receptors at the genomic level. Cancer Res 2013;73:5130-9. [PMID: 23803465 PMCID: PMC3799864 DOI: 10.1158/0008-5472.can-13-0742] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
23
Grøntved L, John S, Baek S, Liu Y, Buckley JR, Vinson C, Aguilera G, Hager GL. C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements. EMBO J 2013;32:1568-83. [PMID: 23665916 DOI: 10.1038/emboj.2013.106] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/10/2013] [Indexed: 01/22/2023]  Open
24
Hakim O, Sung MH, Nakayamada S, Voss TC, Baek S, Hager GL. Spatial congregation of STAT binding directs selective nuclear architecture during T-cell functional differentiation. Genome Res 2012;23:462-72. [PMID: 23212947 PMCID: PMC3589535 DOI: 10.1101/gr.147652.112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
25
Khozoie C, Borland MG, Zhu B, Baek S, John S, Hager GL, Shah YM, Gonzalez FJ, Peters JM. Analysis of the peroxisome proliferator-activated receptor-β/δ (PPARβ/δ) cistrome reveals novel co-regulatory role of ATF4. BMC Genomics 2012;13:665. [PMID: 23176727 PMCID: PMC3556323 DOI: 10.1186/1471-2164-13-665] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 11/22/2012] [Indexed: 12/31/2022]  Open
26
Madrigal P, Krajewski P. Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data. Front Genet 2012;3:230. [PMID: 23118738 PMCID: PMC3484326 DOI: 10.3389/fgene.2012.00230] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 10/13/2012] [Indexed: 12/16/2022]  Open
27
King HA, Trotter KW, Archer TK. Chromatin remodeling during glucocorticoid receptor regulated transactivation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012;1819:716-26. [PMID: 22425674 DOI: 10.1016/j.bbagrm.2012.02.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/24/2012] [Accepted: 02/28/2012] [Indexed: 12/21/2022]
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