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Nucleosome stability measured in situ by automated quantitative imaging

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dc.contributor.author Imre, László
dc.contributor.author Simándi, Zoltán
dc.contributor.author Horváth, Attila
dc.contributor.author Fenyőfalvi, György
dc.contributor.author Nánási, Péter
dc.contributor.author Niaki, Erfaneh Firouzi
dc.contributor.author Hegedüs, Éva
dc.contributor.author Bacsó, Zsolt
dc.contributor.author Weyemi, Urbain
dc.contributor.author Mauser, Rebekka
dc.contributor.author Ausió, Juan
dc.contributor.author Jeltsch, Albert
dc.contributor.author Bonner, William
dc.contributor.author Nagy, László
dc.contributor.author Kimura, Hiroshi
dc.contributor.author Szabó, Gábor
dc.date.accessioned 2019-01-24T20:23:02Z
dc.date.available 2019-01-24T20:23:02Z
dc.date.copyright 2017 en_US
dc.date.issued 2017
dc.identifier.citation Imre, L.; Simándi, Z.; Horváth, A.; Fenyőfalvi, G.; Nánási, P.; Niaki, E. F.; … & Szabó, G. Nucleosome stability measured in situ by automated quantitative imaging. Scientific Reports, 7, article 12734. DOI: 10.1038/s41598-017-12608-9 en_US
dc.identifier.uri https://doi.org/10.1038/s41598-017-12608-9
dc.identifier.uri http://hdl.handle.net/1828/10548
dc.description.abstract Current approaches have limitations in providing insight into the functional properties of particular nucleosomes in their native molecular environment. Here we describe a simple and powerful method involving elution of histones using intercalators or salt, to assess stability features dependent on DNA superhelicity and relying mainly on electrostatic interactions, respectively, and measurement of the fraction of histones remaining chromatin-bound in the individual nuclei using histone type- or posttranslational modification- (PTM-) specific antibodies and automated, quantitative imaging. The method has been validated in H3K4me3 ChIP-seq experiments, by the quantitative assessment of chromatin loop relaxation required for nucleosomal destabilization, and by comparative analyses of the intercalator and salt induced release from the nucleosomes of different histones. The accuracy of the assay allowed us to observe examples of strict association between nucleosome stability and PTMs across cell types, differentiation state and throughout the cell-cycle in close to native chromatin context, and resolve ambiguities regarding the destabilizing effect of H2A.X phosphorylation. The advantages of the in situ measuring scenario are demonstrated via the marked effect of DNA nicking on histone eviction that underscores the powerful potential of topological relaxation in the epigenetic regulation of DNA accessibility. en_US
dc.description.sponsorship The authors thank Adel Nagy Vezendine for conscientious technical assistance and Katrina Good for a careful proofreading of the manuscript. We thank Tom Misteli, NIH, for providing the LacO array system. This work was supported by Hungarian National Science and Research Foundation (OTKA) grants [K72762]; [NK101337]; by TAMOP grants [TAMOP 4.2.2-08/1-2008-0015], [TAMOP 4.2.1/B-09/1/KONV-2010-0007], [TAMOP 4.2.2.A-11/1/KONV-2012-0023 "VED-ELEM"], and [TAMOP 4.2.4.A/2-11-1-2012-0001, GINOP-2.3.2-15-2016-00044, National Excellence Program]', by JSPS KAKENHI, JP 25116005, JP26291071 (to HK) and by Natural Sciences and Engeneering Research Council of Canada (NSERC) 46399-2012 grant (to JA). en_US
dc.language.iso en en_US
dc.publisher Scientific Reports en_US
dc.title Nucleosome stability measured in situ by automated quantitative imaging en_US
dc.type Article en_US
dc.description.scholarlevel Faculty en_US
dc.description.reviewstatus Reviewed en_US


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