DNA structure, nucleosome placement and chromatin remodelling: a perspective

2012 ◽  
Vol 40 (2) ◽  
pp. 335-340 ◽  
Author(s):  
Andrew A. Travers ◽  
Cédric Vaillant ◽  
Alain Arneodo ◽  
Georgi Muskhelishvili
Keyword(s):  
Dna Sequence ◽  
Thermodynamic Stability ◽  
Budding Yeast ◽  
Nucleosome Positioning ◽  
Chromatin Remodelling ◽  
Chromatin Organization ◽  
Eukaryotic Genome ◽  
Major Question ◽  
Chromatin Biology

A major question in chromatin biology is to what extent the sequence of DNA directly determines the genetic and chromatin organization of a eukaryotic genome? We consider two aspects to this question: the DNA sequence-specified positioning of nucleosomes and the determination of NDRs (nucleosome-depleted regions) or barriers. We argue that, in budding yeast, while DNA sequence-specified nucleosome positioning may contribute to positions flanking the regions lacking nucleosomes, DNA thermodynamic stability is a major component determinant of the genetic organization of this organism.

scholarly journals Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

2017 ◽  
Author(s):  
Toru Niina ◽  
Giovanni B. Brandani ◽  
Cheng Tan ◽  
Shoji Takada
Keyword(s):  
Hydrogen Bond ◽  
Dna Sequence ◽  
Base Pair ◽  
Sliding Mode ◽  
Nucleosome Positioning ◽  
Eukaryotic Genome ◽  
Coarse Grained ◽  
Histone Octamer ◽  
Hydrogen Bond Interactions ◽  
Nucleosome Sliding

AbstractWhile nucleosome positioning on eukaryotic genome play important roles for genetic regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood. Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molecular simulation method that incorporates both long-range electrostatic and short-range hydrogen-bond interactions between histone octamer and DNA. The simulations revealed two distinct sliding modes depending on the nucleosomal DNA sequence. A uniform DNA sequence showed frequent sliding with one base pair step in a rotation-coupled manner, akin to screw-like motions. On the contrary, a strong positioning sequence, the so-called 601 sequence, exhibits rare, abrupt transitions of five and ten base pair steps without rotation. Moreover, we evaluated the importance of hydrogen bond interactions on the sliding mode, finding that strong and weak bonds favor respectively the rotation-coupled and -uncoupled sliding movements.Author summaryNucleosomes are fundamental units of chromatin folding consisting of double-stranded DNA wrapped ∼1.7 times around a histone octamer. By densely populating the eukaryotic genome, nucleosomes enable efficient genome compaction inside the cellular nucleus. However, the portion of DNA occupied by a nucleosome can hardly be accessed by other DNA-binding proteins, obstructing fundamental cellular processes such as DNA replication and transcription. DNA compaction and access by other proteins can simultaneously be achieved via the dynamical repositioning of nucleosomes, which can slide along the DNA sequence. In this study, we developed and used coarse-grained molecular dynamics simulations to reveal the molecular details of nucleosome sliding. We find that the sliding mode is highly dependent on the underlying DNA sequence. Specifically, a sequence with a strong nucleosome positioning signal slides via large jumps by five and ten base pairs, preserving the optimal DNA bending profile. On the other hand, uniform sequences without the positioning signal slide via a screw-like motion of DNA, one base pair at the time. These results show that sequence has a large effect not only on the formation of nucleosomes, but also on the kinetics of repositioning.

scholarly journals Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ruifang Guan ◽  
Tengfei Lian ◽  
Bing-Rui Zhou ◽  
Emily He ◽  
Carl Wu ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Chromosome Segregation ◽  
Budding Yeast ◽  
Dna Conformation ◽  
Dependent Manner ◽  
Dynamic Interactions ◽  
Nucleosome Core ◽  
Dynamic Mechanisms ◽  
Nucleosome Formation ◽  
Core Histones

AbstractAccurate chromosome segregation relies on the specific centromeric nucleosome–kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA. The centromeric nucleosome core structure contains 115 base pair DNA including a CCG motif. The CBF3core specifically recognizes the nucleosomal CCG motif through the Gal4 domain while allosterically altering the DNA conformation. Cryo-EM, modeling, and mutational studies reveal that the CBF3core forms dynamic interactions with core histones H2B and CENP-A in the CEN3 nucleosome. Our results provide insights into the structure of the budding yeast centromeric nucleosome and the mechanism of its assembly, which have implications for analogous processes of human centromeric nucleosome formation.

scholarly journals A deformation energy model reveals sequence-dependent property of nucleosome positioning

Chromosoma ◽  
2021 ◽  
Vol 130 (1) ◽  
pp. 27-40
Author(s):  
Guoqing Liu ◽  
Hongyu Zhao ◽  
Hu Meng ◽  
Yongqiang Xing ◽  
Lu Cai
Keyword(s):  
Budding Yeast ◽  
Nucleosome Occupancy ◽  
Nucleosome Positioning ◽  
Deformation Energy ◽  
Energy Model ◽  
Structural Parameter ◽  
High Deformation ◽  
Dna Deformation ◽  
Genome Wide ◽  
Genomic Regions

AbstractWe present a deformation energy model for predicting nucleosome positioning, in which a position-dependent structural parameter set derived from crystal structures of nucleosomes was used to calculate the DNA deformation energy. The model is successful in predicting nucleosome occupancy genome-wide in budding yeast, nucleosome free energy, and rotational positioning of nucleosomes. Our model also indicates that the genomic regions underlying the MNase-sensitive nucleosomes in budding yeast have high deformation energy and, consequently, low nucleosome-forming ability, while the MNase-sensitive non-histone particles are characterized by much lower DNA deformation energy and high nucleosome preference. In addition, we also revealed that remodelers, SNF2 and RSC8, are likely to act in chromatin remodeling by binding to broad nucleosome-depleted regions that are intrinsically favorable for nucleosome positioning. Our data support the important role of position-dependent physical properties of DNA in nucleosome positioning.

scholarly journals Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer

2021 ◽  
Vol 22 (11) ◽  
pp. 5578
Author(s):  
Cedric R. Clapier
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Structural Diversity ◽  
Nucleosome Positioning ◽  
Basic Mechanism ◽  
Progressive Increase ◽  
Chromatin Organization ◽  
Dna Translocation ◽  
Dynamic Regulation ◽  
Cooperative Action

The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions—in particular, the regulation of gene expression—and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.

The first determination of DNA sequence of a specific gene

Gene ◽  
2016 ◽  
Vol 582 (1) ◽  
pp. 94-95
Author(s):  
Masayori Inouye
Keyword(s):  
Dna Sequence ◽  
Specific Gene

scholarly journals Nucleosome Positioning with Set of Key Positions and Nucleosome Affinity

2014 ◽  
Vol 8 (1) ◽  
pp. 166-170 ◽  
Author(s):  
Jia Wang ◽  
Shuai Liu ◽  
Weina Fu
Keyword(s):  
Neural Network ◽  
Experimental Data ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Nucleosome Positioning ◽  
Experimental Results ◽  
Negative Effects ◽  
Sequence Structure ◽  
Precise Positioning ◽  
Histone Octamer

The formation and precise positioning of nucleosome in chromatin occupies a very important role in studying life process. Today, there are many researchers who discovered that the positioning where the location of a DNA sequence fragment wraps around a histone octamer in genome is not random but regular. However, the positioning is closely relevant to the concrete sequence of core DNA. So in this paper, we analyzed the relation between the affinity and sequence structure of core DNA, and extracted the set of key positions. In these positions, the nucleotide sequences probably occupy mainly action in the binding. First, we simplified and formatted the experimental data with the affinity. Then, to find the key positions in the wrapping, we used neural network to analyze the positive and negative effects of nucleosome generation for each position in core DNA sequences. However, we reached a class of weights with every position to describe this effect. Finally, based on the positions with high weights, we analyzed the reason why the chosen positions are key positions, and used these positions to construct a model for nucleosome positioning prediction. Experimental results show the effectiveness of our method.

scholarly journals Determination of thermodynamic stability of FeB monoboride

2019 ◽  
Vol 27 (2) ◽  
pp. 69-76
Author(s):  
N. Yu. Filonenko ◽  
A. N. Galdina
Keyword(s):  
Thermodynamic Stability ◽  
Boron Content ◽  
Boron Concentration ◽  
Cast Alloy ◽  
Thermodynamic Characteristics ◽  
X Ray Diffraction ◽  
X Ray ◽  
High Temperature Expansion ◽  
Experimental Findings

In this paper we investigate the phase composition and phase transformations in the Fe-B system alloys with boron content in the range of 9.0–15.0 wt.%. We use microstructural, X-ray diffraction, differential thermal and durometric analyzes to determine the physical properties of the alloys. The experimental findings show that in the as-cast alloy structure there is Fe5B3 phase in small quantities along with FeB monoboride and Fe2B boride. The Fe5B3 phase is formed as a result of the peritectic reaction L+FeB→Fe5B3 at the temperature of 1680 K. The eutectic transformation L→Fe5B3 +Fe2B occurs in the boron concentration range of 8.8–10.5 wt.%. After annealing of the Fe-B alloys at the temperature of 1473 K and cooling with the rate of 102 K/s we observe the occurring of the Fe5B3 phase. To spot an opportunity of the secondary monoboride formation in the alloys under consideration, we calculate the thermodynamic characteristics of stability of the system. Accounting for the contribution of the first degree approximation of high-temperature expansion of thermodynamic potential of FeB iron monoboride in a Fe-B binary alloy enables us to study its thermodynamic stability. It is shown that stability decrease of FeB at 1423 K allows suggesting that at this temperature the phase transformation occurs and this fact correlates to the differential thermal analysis results.

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