Ofir Hakim Lab
Epigenomics of Gene Regulation in 3D
Epigenomics of Gene Regulation in 3D
Publications
2020
Schwartz M, Sarusi Portugez A, Zukerman Attia B, Tannenbaum M, Cohen L, Loza O, Chase E, Turman Y, Kaplan T, Salah Z & Hakim O, Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation. Commun Biol 3, 696 (2020). https://doi.org/10.1038/s42003-020-01398-y
Krispil R, Tannenbaum M, Sarusi-Portuguez A, Loza O, Raskina O, Hakim O, The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE, Internation Journal of Molecular Sciences Int. J. Mol. Sci. 2020 210.3390/ijms21072373
2019
2015
Tannenbaum M, Sarusi-Portuguez A, Krispil R, Schwartz M, Loza O, Benichou JI, Mosquna A, Hakim O, Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq, Plant Methods 2018 14(1):113
2017
2016
Weizman E, Tannenbaum M, Tarrant A, Hakim O, Levy O., Chromatin dynamics enable transcriptional rhythms in the cnidarian Nematostella vectensis, PLoS Genetics 2019 10.1371/journal.pgen
2018
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Sheinboim D, Maza I, Dror I, Parikh S, Krupalnik V, Bell RE, Zviran A, Suita Y, Hakim O, Mandel-Gutfreund Y, Khaled M, Hanna JH, Levy C. OCT4 impedes cell fate redirection by the melanocyte lineage master regulator MITF in mouse ESCs. Nat. Commun. 2017 Oct 18;8(1):1022.
Sarusi Portuguez A, 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 Oct;284(19):3230-3244.
Grbesa I, Tannenbaum M, Sarusi-Portuguez A, Schwartz M, Hakim O. Mapping Genome-Wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq. JoVE. 2017 Nov 13;(129).
Grbesa I, Hakim O. Genomic effects of glucocorticoids. Protoplasma. 2017 May 1;254(3):1175-1185.
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Oliva M, Butenko Y, Hsieh TF, Hakim O, Katz A, Smorodinsky NI, Michaeli D, Fischer RL, Ohad N. FIE, a nuclear PRC2 protein, forms cytoplasmic complexes in Arabidopsis thaliana. J Exp Bot. 2016 Nov 1;67(21):6111-6123.
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Sams DS, Nardone S, Getselter D, Raz D, Tal M, Rayi PR, Kaphzan H, Hakim O, Elliott E. Neuronal CTCF Is Necessary for Basal and Experience-Dependent Gene Regulation, Memory Formation, and Genomic Structure of BDNF and Arc. Cell Rep. 2016 Nov 22;17(9):2418-2430.
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Wang Q, Sawyer IA, Sung MH, Sturgill D, Shevtsov SP, Pegoraro G, Hakim O, Baek S, Hager GL, Dundr M(2016). Cajal bodies are linked to genome conformation. Nat.Commun. 2016 Mar 21;7:10966.
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Schwartz M, Sarusi A, Deitch RT, Tal M, Raz D, Sung MH, Kaplan T, Hakim O. Comparative analysis of ligases and polymerases used in chromosome conformation capture assays. BioTechniques. 2015 Apr 1;58(4):195-9.
2014
Schwartz M, Hakim O. 3D view of chromosomes, DNA damage, and translocations. Curr Opin Genet Dev. 2014 Mar 12;25C:118-125
2013
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. 2013 Dec 19;155(7):1507-20.
Aguilar-Arnal L, Hakim O, Patel VR, Baldi P, Hager GL, Sassone-Corsi P. Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nat Struct Mol Biol. 2013 Oct;20(10):1206-13.
Casellas R, Resch W, Hakim O, Nussenzweig MC. The origin of B cell recurrent chromosomal translocations: proximity versus DNA damage. Mol Cell. 2013 Aug 8;51(3):275-6.
Nakahashi H, Kwon KR, Resch W, Vian L, Dose M, Stavreva D, Hakim O, Pruett N, Nelson S, Yamane A, Qian J, Dubois W, Welsh S, Phair RD, Pugh BF, Lobanenkov V, Hager GL, Casellas R. A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Rep. 2013 May 30;3(5):1678-89.
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. 2013 Mar;23(3):462-72.
2012
2011
Kovalchuk AL, Ansarah-Sobrinho C, Hakim O, Resch W, Tolarová H, Dubois W, Yamane A, Takizawa M, Klein I, Hager GL, Morse HC 3rd, Potter M, Nussenzweig MC, Casellas R. Mouse model of endemic Burkitt translocations reveals the long-range boundaries of Ig-mediated oncogene deregulation. Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10972-7.
Hakim O, Misteli T. SnapShot: Chromosome confirmation capture. Cell. 2012 Mar 2;148(5):1068.e1-2.
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Hakim O, Resch W, Yamane A, Klein I, Kieffer-Kwon KR, Jankovic M, Oliveira T, Bothmer A, Voss TC, Ansarah-Sobrinho C, Mathe E, Liang G, Cobell J, Nakahashi H, Robbiani DF, Nussenzweig A, Hager GL, Nussenzweig MC, Casellas R. DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature. 2012 Feb 7;484(7392):69-74.
Nakayamada S, Kanno Y, Takahashi H, Jankovic D, Lu KT, Johnson TA, Sun HW, Vahedi G, Hakim O, Handon R, Schwartzberg PL, Hager GL, O'Shea JJ. Early Th1 cell differentiation is marked by a Tfh cell-like transition. Immunity. 2011 Dec 23;35(6):919-31.
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Hakim O, Sung MH, Voss TC, Splinter E, John S, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, de Laat W, Hager GL. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 2011 May;21(5):697-706.
2010
Hakim O, Sung MH, Hager GL. 3D shortcuts to gene regulation. Curr Opin Cell Biol. 2010 Jun;22(3):305-13.
2009
Hakim O, John S, Ling JQ, Biddie SC, Hoffman AR, Hager GL. Glucocorticoid receptor activation of the Ciz1-Lcn2 locus by long range interactions. J Biol Chem. 2009 Mar 6;284(10):6048-52.
2022
Avital Sarusi Portuguez , Ivana Grbesa , Moran Tal , Rachel Deitch , Dana Raz , Limor Kliker , Ran Weismann , Michal Schwartz , Olga Loza , Leslie Cohen , Libi Marchenkov-Flam , Myong-Hee Sung , Tommy Kaplan , Ofir Hakim , Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression. DOI: 10.1093/nar/gkac488
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