Mechanistic Analyses of Supercoiling Behaviors of DNA in Nucleosomes and Chromatins

Mapping Intimacies ◽

10.1101/523084 ◽

2019 ◽

Author(s):

Hao Zhang ◽

Tianhu Li

Keyword(s):

Dna Sequences ◽

Base Pair ◽

Histone H1 ◽

Molecular Pathways ◽

Core Particle ◽

Nucleosome Core Particle ◽

Nucleosome Core ◽

Histone Octamers ◽

Dynamic Structures ◽

Current Report

AbstractBesides those in 146-base pair nucleosome core particle DNA, supercoils have been known to be present in 10-base pair arm DNA segments and naked linker DNA segments. The interacting patterns among histone octamers, histone H1, 10-base pair arm DNA segments and linker DNA have, however, not yet been elucidated. In the current report, we examine correlations among constituents of nucleosomes from the mechanistic perspectives and present molecular pathways for elucidating supercoiling behaviors of their component DNA sequences. It is our hope that our new analyses could serve as incentives to further clarify correlations between histones and DNA in the dynamic structures of chromatins in the future.

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Helical repeat of DNA in the nucleosome core particle

Biochemical Society Transactions ◽

10.1042/bst0280373 ◽

2000 ◽

Vol 28 (4) ◽

pp. 373-376 ◽

Cited By ~ 2

Author(s):

R. Negri ◽

M. Buttinelli ◽

G. Panetta ◽

V. De Arcangelis ◽

E. Di Mauro ◽

...

Keyword(s):

Dna Sequences ◽

Linker Histone ◽

Core Particle ◽

Nucleosome Core Particle ◽

Apparent Paradox ◽

Nucleosome Core ◽

Nucleosome Core Particles ◽

High Affinity Site ◽

Hydroxyl Radical Cleavage ◽

Radical Cleavage

Although the crystal structure of nucleosome core particle is essentially symmetrical in the vicinity of the dyad, the linker histone binds asymmetrically in this region to select a single high-affinity site from potentially two equivalent sites. To try to resolve this apparent paradox we mapped to base-pair resolution the dyads and rotational settings of nucleosome core particles reassembled on synthetic tandemly repeating 20 bp DNA sequences. In agreement with previous observations, we observed (1) that the helical repeat on each side of the dyad cluster is 10 bp maintaining register with the sequence repeat and (2) that this register changes by 2 bp in the vicinity of the dyad. The additional 2 bp required to effect the change in the rotational settings is accommodated by an adjustment immediately adjacent to the dyad. At the dyad the hydroxyl radical cleavage is asymmetric and we suggest that the inferred structural asymmetry could direct the binding of the linker histone to a single preferred site.

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X-ray structure of the MMTV-A nucleosome core

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1524607113 ◽

2016 ◽

Vol 113 (5) ◽

pp. 1214-1219 ◽

Cited By ~ 25

Author(s):

Timothy D. Frouws ◽

Sylwia C. Duda ◽

Timothy J. Richmond

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Promoter Sequence ◽

Core Particle ◽

Nucleosome Core Particle ◽

Particle Structure ◽

X Ray ◽

Nucleosome Core ◽

Sequence Dependent

The conformation of DNA bound in nucleosomes depends on the DNA sequence. Questions such as how nucleosomes are positioned and how they potentially bind sequence-dependent nuclear factors require near-atomic resolution structures of the nucleosome core containing different DNA sequences; despite this, only the DNA for two similar α-satellite sequences and a sequence (601) selected in vitro have been visualized bound in the nucleosome core. Here we report the 2.6-Å resolution X-ray structure of a nucleosome core particle containing the DNA sequence of nucleosome A of the 3′-LTR of the mouse mammary tumor virus (147 bp MMTV-A). To our knowledge, this is the first nucleosome core particle structure containing a promoter sequence and crystallized from Mg2+ ions. It reveals sequence-dependent DNA conformations not seen previously, including kinking into the DNA major groove.

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