The bending of DNA in nucleosomes and its wider implications

1987 ◽  
Vol 317 (1187) ◽  
pp. 537-561 ◽  
Keyword(s):  
Dna Sequences ◽  
Nucleosome Core Particle ◽  
Base Pairs ◽  
Structural Explanation ◽  
Bent Dna ◽  
Nucleosome Core ◽  
Histone Octamer ◽  
Naturally Occurring ◽  
Superhelical Turn ◽  
Intrinsically Bent Dna

The DNA of a nucleosome core particle is wrapped tightly around a histone octamer with approximately 80 base pairs per superhelical turn. Studies of both naturally occurring and reconstituted systems have shown that DNA sequences very often adopt well-defined locations with respect to the octamer. Recent work in this laboratory has provided a structural explanation for this sequence-dependent positioning in terms of the differential flexibility of different sequences and of departures from smooth bending. The ‘rules’ that are emerging for DNA bendability and, from the results of other workers, on intrinsically bent DNA, are likely to be useful in considering looping and bending of DNA in other processes in which it is thought to be wrapped around a protein core.

Helical repeat of DNA in the nucleosome core particle

2000 ◽  
Vol 28 (4) ◽  
pp. 373-376 ◽  
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.

scholarly journals DNA information: from digital code to analogue structure

2012 ◽  
Vol 370 (1969) ◽  
pp. 2960-2986 ◽  
Author(s):  
A. A. Travers ◽  
G. Muskhelishvili ◽  
J. M. T. Thompson
Keyword(s):  
Dimensional Space ◽  
Double Helix ◽  
Three Dimensional ◽  
Base Pairs ◽  
Nucleosome Core ◽  
Histone Octamer ◽  
Regulatory Mode ◽  
Sequence Periodicity ◽  
Recent Developments ◽  
Dna Double Helix

The digital linear coding carried by the base pairs in the DNA double helix is now known to have an important component that acts by altering, along its length, the natural shape and stiffness of the molecule. In this way, one region of DNA is structurally distinguished from another, constituting an additional form of encoded information manifest in three-dimensional space. These shape and stiffness variations help in guiding and facilitating the DNA during its three-dimensional spatial interactions. Such interactions with itself allow communication between genes and enhanced wrapping and histone–octamer binding within the nucleosome core particle. Meanwhile, interactions with proteins can have a reduced entropic binding penalty owing to advantageous sequence-dependent bending anisotropy. Sequence periodicity within the DNA, giving a corresponding structural periodicity of shape and stiffness, also influences the supercoiling of the molecule, which, in turn, plays an important facilitating role. In effect, the super-helical density acts as an analogue regulatory mode in contrast to the more commonly acknowledged purely digital mode. Many of these ideas are still poorly understood, and represent a fundamental and outstanding biological question. This review gives an overview of very recent developments, and hopefully identifies promising future lines of enquiry.

scholarly journals X-ray structure of the MMTV-A nucleosome core

2016 ◽  
Vol 113 (5) ◽  
pp. 1214-1219 ◽  
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.

scholarly journals The prenucleosome, a stable conformational isomer of the nucleosome

2015 ◽  
Vol 29 (24) ◽  
pp. 2563-2575 ◽  
Author(s):  
Jia Fei ◽  
Sharon E. Torigoe ◽  
Christopher R. Brown ◽  
Mai T. Khuong ◽  
George A. Kassavetis ◽  
...  
Keyword(s):  
Motor Protein ◽  
Upstream Region ◽  
Entry And Exit ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Nucleosome Core ◽  
Histone Octamer ◽  
Conformational Isomer

Chromatin comprises nucleosomes as well as nonnucleosomal histone–DNA particles. Prenucleosomes are rapidly formed histone–DNA particles that can be converted into canonical nucleosomes by a motor protein such as ACF. Here we show that the prenucleosome is a stable conformational isomer of the nucleosome. It consists of a histone octamer associated with ∼80 base pair (bp) of DNA, which is located at a position that corresponds to the central 80 bp of a nucleosome core particle. Monomeric prenucleosomes with free flanking DNA do not spontaneously fold into nucleosomes but can be converted into canonical nucleosomes by an ATP-driven motor protein such as ACF or Chd1. In addition, histone H3K56, which is located at the DNA entry and exit points of a canonical nucleosome, is specifically acetylated by p300 in prenucleosomes relative to nucleosomes. Prenucleosomes assembled in vitro exhibit properties that are strikingly similar to those of nonnucleosomal histone–DNA particles in the upstream region of active promoters in vivo. These findings suggest that the prenucleosome, the only known stable conformational isomer of the nucleosome, is related to nonnucleosomal histone–DNA species in the cell.

scholarly journals Mechanistic Analyses of Supercoiling Behaviors of DNA in Nucleosomes and Chromatins

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.

How does the histone code work?

2005 ◽  
Vol 83 (4) ◽  
pp. 468-476 ◽  
Author(s):  
Michael S Cosgrove ◽  
Cynthia Wolberger
Keyword(s):  
Chromatin Structure ◽  
Histone Code ◽  
Globular Domain ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Histone Tails ◽  
Post Translational Modifications ◽  
Nucleosome Core ◽  
Histone Octamer ◽  
Nucleosome Dynamics

Patterns of histone post-translational modifications correlate with distinct chromosomal states that regulate access to DNA, leading to the histone-code hypothesis. However, it is not clear how modification of flexible histone tails leads to changes in nucleosome dynamics and, thus, chromatin structure. The recent discovery that, like the flexible histone tails, the structured globular domain of the nucleosome core particle is also extensively modified adds a new and exciting dimension to the histone-code hypothesis, and calls for the re-examination of current models for the epigenetic regulation of chromatin structure. Here, we review these findings and other recent studies that suggest the structured globular domain of the nucleosome core particle plays a key role regulating chromatin dynamics.Key words: histones, histone code, modifications, epigenetic, chromatin, nucleosome, dynamics, regulated nucleosome mobility, core, archaeal, combinatorial switch, histone octamer.

Sign in / Sign up

Export Citation Format

Share Document