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J Biol Chem. 2019 Mar 15;294(11):4233-4246. doi: 10.1074/jbc.RA118.006412. Epub 2019 Jan 10.

Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays.

Author information

1
From the Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033.
2
Biological Faculty, Department of Molecular Biology, Lomonosov Moscow State University, 119192 Moscow, Russia, and.
3
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.
4
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 zhurkin@nih.gov.
5
From the Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, sag17@psu.edu.

Abstract

The length of linker DNA that separates nucleosomes is highly variable, but its mechanistic role in modulating chromatin structure and functions remains unknown. Here, we established an experimental system using circular arrays of positioned nucleosomes to investigate whether variations in nucleosome linker length could affect nucleosome folding, self-association, and interactions. We conducted EM, DNA topology, native electrophoretic assays, and Mg2+-dependent self-association assays to study intrinsic folding of linear and circular nucleosome arrays with linker DNA length of 36 bp and 41 bp (3.5 turns and 4 turns of DNA double helix, respectively). These experiments revealed that potential artifacts arising from open DNA ends and full DNA relaxation in the linear arrays do not significantly affect overall chromatin compaction and self-association. We observed that the 0.5 DNA helical turn difference between the two DNA linker lengths significantly affects DNA topology and nucleosome interactions. In particular, the 41-bp linkers promoted interactions between any two nucleosome beads separated by one bead as expected for a zigzag fiber, whereas the 36-bp linkers promoted interactions between two nucleosome beads separated by two other beads and also reduced negative superhelicity. Monte Carlo simulations accurately reproduce periodic modulations of chromatin compaction, DNA topology, and internucleosomal interactions with a 10-bp periodicity. We propose that the nucleosome spacing and associated chromatin structure modulations may play an important role in formation of different chromatin epigenetic states, thus suggesting implications for how chromatin accessibility to DNA-binding factors and the RNA transcription machinery is regulated.

KEYWORDS:

DNA topology; chromatin higher order structure; chromatin structure; computer modeling; conformational simulation; electron microscopy (EM); epigenetic regulation; epigenetics; gene regulation; histone; linker DNA; nucleosome

PMID:
30630950
PMCID:
PMC6422092
[Available on 2020-03-15]
DOI:
10.1074/jbc.RA118.006412
[Indexed for MEDLINE]

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