Nucleosome stability measured in situ by automated quantitative imaging




Imre, László
Simándi, Zoltán
Horváth, Attila
Fenyőfalvi, György
Nánási, Péter
Niaki, Erfaneh Firouzi
Hegedüs, Éva
Bacsó, Zsolt
Weyemi, Urbain
Mauser, Rebekka

Journal Title

Journal ISSN

Volume Title


Scientific Reports


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.




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