Single-molecule compaction of megabase-long chromatin molecules by multivalent cations

• Published in: Nucleic acids research Vol. 46; no. 2; pp. 635 - 649
• Main Authors: Zinchenko, Anatoly, Berezhnoy, Nikolay V, Wang, Sai, Rosencrans, William M, Korolev, Nikolay, van der Maarel, Johan R C, Nordenskiöld, Lars
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 25-01-2018
• Subjects: Bacteriophage T4 - genetics; Cations - chemistry; Cations - metabolism; Chromatin - chemistry; Chromatin - genetics; Chromatin - metabolism; DNA, Viral - chemistry; DNA, Viral - genetics; DNA, Viral - metabolism; Gene regulation, Chromatin and Epigenetics; Histones - chemistry; Histones - genetics; Histones - metabolism; Humans; Microscopy, Atomic Force; Microscopy, Electron, Transmission; Microscopy, Fluorescence; Nucleic Acid Conformation; Nucleosomes - chemistry; Nucleosomes - genetics; Nucleosomes - metabolism; Single Molecule Imaging - methods
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkx1135

Abstract
To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250-400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo. Variation of HO loading revealed a number of unique features related to the efficiency of chromatin compaction by multivalent cations, the mechanism of compaction, and the character of partly compact chromatin structures. The observations may be relevant for how DNA accessibility in chromatin is maintained. Compaction of saturated chromatin, in turn, is accompanied by an intra-chain segregation at the level of single chromatin molecules, suggesting an intriguing scenario of selective activation/deactivation of DNA as a result of chromatin fiber heterogeneity due to the nucleosome positioning. We suggest that this chromatin, reconstituted on megabase-long DNA because of its large size, is a useful model of eukaryotic chromatin.