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For: Wen B, Wu H, Loh YH, Briem E, Daley GQ, Feinberg AP. Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions. BMC Genomics 2012;13:566. [PMID: 23102236 PMCID: PMC3507770 DOI: 10.1186/1471-2164-13-566] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 10/19/2012] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Spracklin G, Abdennur N, Imakaev M, Chowdhury N, Pradhan S, Mirny LA, Dekker J. Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Nat Struct Mol Biol 2023;30:38-51. [PMID: 36550219 PMCID: PMC9851908 DOI: 10.1038/s41594-022-00892-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/01/2022] [Indexed: 12/24/2022]
2
Gaspar AD, Cuddapah S. Nickel-induced alterations to chromatin structure and function. Toxicol Appl Pharmacol 2022;457:116317. [PMID: 36400264 PMCID: PMC9722551 DOI: 10.1016/j.taap.2022.116317] [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: 08/03/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
3
Velay F, Méteignier LV, Laloi C. You shall not pass! A Chromatin barrier story in plants. FRONTIERS IN PLANT SCIENCE 2022;13:888102. [PMID: 36212303 PMCID: PMC9540200 DOI: 10.3389/fpls.2022.888102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
4
van Schaik T, Liu NQ, Manzo SG, Peric-Hupkes D, de Wit E, van Steensel B. CTCF and cohesin promote focal detachment of DNA from the nuclear lamina. Genome Biol 2022;23:185. [PMID: 36050765 PMCID: PMC9438259 DOI: 10.1186/s13059-022-02754-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 08/22/2022] [Indexed: 01/23/2023]  Open
5
Yan Z, Ji L, Huo X, Wang Q, Zhang Y, Wen B. G9a/GLP-sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020;18:359-370. [PMID: 33285284 PMCID: PMC8242262 DOI: 10.1016/j.gpb.2020.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/01/2020] [Accepted: 10/26/2020] [Indexed: 11/30/2022]
6
Myasoedova VA, Sukhorukov V, Grechko AV, Zhang D, Romanenko E, Orekhov V, Orekhov AN. Inhibitors of DNA Methylation and Histone Deacetylation as Epigenetically Active Drugs for Anticancer Therapy. Curr Pharm Des 2020;25:635-641. [PMID: 30950345 DOI: 10.2174/1381612825666190405144026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/29/2019] [Indexed: 12/12/2022]
7
Çelik-Uzuner S. Enhanced immunological detection of epigenetic modifications of DNA in healthy and cancerous cells by fluorescence microscopy. Microsc Res Tech 2019;82:1962-1972. [PMID: 31429164 DOI: 10.1002/jemt.23365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022]
8
Current epigenetic aspects the clinical kidney researcher should embrace. Clin Sci (Lond) 2017;131:1649-1667. [DOI: 10.1042/cs20160596] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 02/06/2023]
9
Madakashira BP, Sadler KC. DNA Methylation, Nuclear Organization, and Cancer. Front Genet 2017. [PMID: 28638402 PMCID: PMC5461260 DOI: 10.3389/fgene.2017.00076] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
10
Christogianni A, Chatzantonaki E, Soupsana K, Giannios I, Platania A, Politou AS, Georgatos S. Heterochromatin remodeling in embryonic stem cells proceeds through stochastic de-stabilization of regional steady-states. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017;1860:661-673. [DOI: 10.1016/j.bbagrm.2017.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/19/2016] [Accepted: 01/19/2017] [Indexed: 01/10/2023]
11
Potential energy landscapes identify the information-theoretic nature of the epigenome. Nat Genet 2017;49:719-729. [PMID: 28346445 PMCID: PMC5565269 DOI: 10.1038/ng.3811] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/13/2017] [Indexed: 12/11/2022]
12
Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis. Nat Genet 2017;49:367-376. [PMID: 28092686 DOI: 10.1038/ng.3753] [Citation(s) in RCA: 319] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 11/28/2016] [Indexed: 12/13/2022]
13
CUDR promotes liver cancer stem cell growth through upregulating TERT and C-Myc. Oncotarget 2016;6:40775-98. [PMID: 26513297 PMCID: PMC4747368 DOI: 10.18632/oncotarget.5805] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/20/2015] [Indexed: 01/01/2023]  Open
14
Isbel L, Prokopuk L, Wu H, Daxinger L, Oey H, Spurling A, Lawther AJ, Hale MW, Whitelaw E. Wiz binds active promoters and CTCF-binding sites and is required for normal behaviour in the mouse. eLife 2016;5. [PMID: 27410475 PMCID: PMC4977153 DOI: 10.7554/elife.15082] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/09/2016] [Indexed: 12/26/2022]  Open
15
Wei Y, Wu H. Measuring the spatial correlations of protein binding sites. Bioinformatics 2016;32:1766-72. [PMID: 26861822 DOI: 10.1093/bioinformatics/btw058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 01/25/2016] [Indexed: 11/14/2022]  Open
16
Gonzalez-Sandoval A, Gasser SM. On TADs and LADs: Spatial Control Over Gene Expression. Trends Genet 2016;32:485-495. [PMID: 27312344 DOI: 10.1016/j.tig.2016.05.004] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 01/10/2023]
17
Dere E, Huse S, Hwang K, Sigman M, Boekelheide K. Intra- and inter-individual differences in human sperm DNA methylation. Andrology 2016;4:832-42. [PMID: 27089098 DOI: 10.1111/andr.12170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/06/2016] [Accepted: 01/13/2016] [Indexed: 12/20/2022]
18
Fu Y, Lv P, Yan G, Fan H, Cheng L, Zhang F, Dang Y, Wu H, Wen B. MacroH2A1 associates with nuclear lamina and maintains chromatin architecture in mouse liver cells. Sci Rep 2015;5:17186. [PMID: 26603343 PMCID: PMC4658601 DOI: 10.1038/srep17186] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/26/2015] [Indexed: 12/26/2022]  Open
19
Mosquera Orgueira A. Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways. Front Genet 2015;6:163. [PMID: 26029238 PMCID: PMC4429616 DOI: 10.3389/fgene.2015.00163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 04/10/2015] [Indexed: 12/31/2022]  Open
20
Talamas JA, Capelson M. Nuclear envelope and genome interactions in cell fate. Front Genet 2015;6:95. [PMID: 25852741 PMCID: PMC4365743 DOI: 10.3389/fgene.2015.00095] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 02/22/2015] [Indexed: 12/14/2022]  Open
21
Harr JC, Luperchio TR, Wong X, Cohen E, Wheelan SJ, Reddy KL. Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins. ACTA ACUST UNITED AC 2015;208:33-52. [PMID: 25559185 PMCID: PMC4284222 DOI: 10.1083/jcb.201405110] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
22
Epigenetic dysregulation by nickel through repressive chromatin domain disruption. Proc Natl Acad Sci U S A 2014;111:14631-6. [PMID: 25246589 DOI: 10.1073/pnas.1406923111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
23
Lyons DB, Lomvardas S. Repressive histone methylation: a case study in deterministic versus stochastic gene regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014;1839:1373-84. [PMID: 24859457 DOI: 10.1016/j.bbagrm.2014.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/09/2014] [Accepted: 05/13/2014] [Indexed: 01/21/2023]
24
Genome regulation at the peripheral zone: lamina associated domains in development and disease. Curr Opin Genet Dev 2014;25:50-61. [PMID: 24556270 DOI: 10.1016/j.gde.2013.11.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/29/2013] [Indexed: 12/18/2022]
25
Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP. Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization. Genome Res 2013;24:177-84. [PMID: 24068705 PMCID: PMC3912409 DOI: 10.1101/gr.157743.113] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
26
Timp W, Feinberg AP. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer 2013;13:497-510. [PMID: 23760024 PMCID: PMC4636434 DOI: 10.1038/nrc3486] [Citation(s) in RCA: 410] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
27
Towbin BD, Gonzalez-Sandoval A, Gasser SM. Mechanisms of heterochromatin subnuclear localization. Trends Biochem Sci 2013;38:356-63. [PMID: 23746617 DOI: 10.1016/j.tibs.2013.04.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/24/2013] [Accepted: 04/30/2013] [Indexed: 11/18/2022]
28
The potential for stem cells in cerebral palsy--piecing together the puzzle. Semin Pediatr Neurol 2013;20:146-53. [PMID: 23948689 DOI: 10.1016/j.spen.2013.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
29
Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev 2013;113:8683-705. [PMID: 23597155 DOI: 10.1021/cr300513p] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
30
Ho AS, Turcan S, Chan TA. Epigenetic therapy: use of agents targeting deacetylation and methylation in cancer management. Onco Targets Ther 2013;6:223-32. [PMID: 23569385 PMCID: PMC3615839 DOI: 10.2147/ott.s34680] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
31
Tarakhovsky A. Logic of the inflammation-associated transcriptional response. Adv Immunol 2013;119:107-33. [PMID: 23886066 DOI: 10.1016/b978-0-12-407707-2.00004-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
32
Reddy KL, Feinberg AP. Higher order chromatin organization in cancer. Semin Cancer Biol 2012;23:109-15. [PMID: 23266653 DOI: 10.1016/j.semcancer.2012.12.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 12/12/2012] [Indexed: 01/30/2023]
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