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Search Results: 1 - 10 of 298630 matches for " nucleosome<br> "
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Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

Duan Zhao-Wen,Li Wei,Xie Ping,Dou Shuo-Xing,Wang Peng-Ye,

中国物理 B , 2010,
Abstract: Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the ``cross-talking' interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.
The Impact of Gene Function on Nucleosome Positioning in the Absence of ISW2

胡焕, 丰继华, 魏恨恨, 周晓雯, 李泽华
Biophysics (BIPHY) , 2015, DOI: 10.12677/BIPHY.2015.34007
To study the impact of chromatin remodeling factor on nucleosome positioning and the function of gene in the formation of nucleosomes in the absence of ISW2, this paper compares and analyzes the data on the proportion of nucleosomes in three kinds of yeasts, which are cultured without ISW2, WT or in YPD. The study finds that in the absence of ISW2 the nuclesomes are far from TSS and that 11 genes impose noticeable impact on nuclesome positioning.
Nicotiana ovule extracts induce nuclear reconstitution of demembranated Xenopus sperm in cell-free system

Ping Lu,Min Ren,Zhonghe Zhai,

科学通报(英文版) , 2002,
Abstract: Nicotiana tabaccum ovule extracts induced nuclear reconstitution of demembranated Xenopus leavis sperm in a cell-free system. Demembranated Xenopus sperm began to swell after 15 min of incubation with Nicotiana ovule extracts. Accompanying the process of incubation, Xenopus sperm decondensed and their shapes changed gradually from long and ellipse to round. The completely decondensed chromatin was surrounded with membrane structure, which was a mixture envelope of a double membrane and a single membrane. Nucleosome assembly was verified by means of micrococcal nuclease digestion to reconstituted nuclei and DNA electrophoresis. Nicotiana ovule extracts supplied one more experimental model and system. The new system could promote powerfully the research on mechanisms of cell division and cell cycle regulation.
Qing Li in Peking University Has Progress about the Mechanism in DNA Replication-Coupled Nucleosome Assemble

Biodiscovery CNS (BDCNS) , 2017, DOI: 10.12677/bdcns.2017.11005
Abstract: [Science系列] 北京大学生命科学学院、北京大学-清华大学生命科学联合中心研究员李晴研究组近日在DNA复制偶联的核小体组装的机制方面做出重要突破,该工作发现单链DNA结合蛋白RPA通过结合组蛋白H3-H4,形成一个高效的平台递呈组蛋白到新合成子链起始核小体组装。这一发现揭示一条全新的DNA复制和核小体组装的偶联机制,大大促进染色质复制领域的发展。该成果发表在2017年1月27号的《科学》(Science)上(RPA binds histone H3-H4 and functions in DNA replication-coupled nucleosome assembly)。
Advances in Nucleosome Positioning

生物物理学报 , 2009,
Abstract: 核小体定位在诸如转录调控、DNA复制和修复等多种细胞过程中起着重要作用。基因组上核小体位置的确定涉及DNA、转录因子、组蛋白修饰酶和染色质重塑复合体之间的相互作用。核小体定位、组蛋白修饰、染色质重塑等问题已成为目前遗传学研究的热点——表观遗传学——的重要研究内容。文章从核小体定位基本概念、核小体定位与基因表达调控的关系、核小体定位实验研究和理论预测工作等几个方面总结了核小体定位的最新研究进展。
Nuclear reassembly in vitro is independent of nucleosome/chromatin assembly

JIANG Zhengfan,ZHANG Bo,ZHAI Zhonghe,

中国科学C辑(英文版) , 1998,
Abstract: It was show11 that nuclear reassembly was induced by small pieces of DNA fragments in cell-free extracts ofXenopus. In an attempt to learn the relationship between the nuclear reassembly and nucleosome/chromatin assembly, limited amounts of CM-Cellulose are used to eliminate the capacity of the egg extract S-150 to assemble chromatin. while the forming of nucleosomes is checked with DNA supercoiling by plasmid DNA pBR322 incubated in the extract, and further analysed by micrococcal nuclease digestion. This depleted extract is then used to induce nuclear reassembly around demembraned sperms with membrane vesicles. It is found that CM-Cellulose depletes histones H2A and H2B efficiently and blocks the assembly of nucleosomes, the demembraned sperms are yet reconstituted into nuclei in the treated S-150, although the chromatin in reassembled nuclei does not produce protected DNA fragments when digested with micrococcal nuclease. It suggests that in the cell-free system ofXenopus, DNA can be formed into nuclei without assembly of nucleosomes or chromatin. Projrrt supported by the National Natural Science Foundation of China (Grant No. 39730240)
Interactions between HMG proteins and the core sequence of DNaseI hypersensitive site 2 in the locus control region (LCR) of the human β-like globin gene cluster

ZHAO Hui,ZHANG Shubing,JIANG Chu,QIAN Ruolan,

中国科学C辑(英文版) , 2000,
Abstract: HMG proteins are abundant chromosomal non-histone proteins. It has been suggested that the HMG proteins may play an important role in the structure and function of chromatin. In the present study, the binding of HMG proteins (HMG1/2 and HMG14/17) to the core DNA sequence of DNaseI hypersensitive site 2 (HS2core DNA sequence, -10681-10970 bp) in the locus control region (LCR) of the human β-like globin gene cluster has been examined by using both thein vitro nucleosome reconstitution and the gel mobility shift assays. Here we show that HMG1/2 can bind to the naked HS2core DNA sequence, however, HMG14/17 cannot. Using thein vitro nucleosome reconstitution we demonstrate that HMG14/17 can bind to the HS2core DNA sequence which is assembled into nucleosomes with the core histone octamer transferred from chicken erythrocytes. In contrast, HMG1/2 cannot bind to the nucleosomes reconstitutedin vitro with the HS2core DNA sequence. These results indicate that the binding patterns between HMG proteins and the HS2core DNA sequence which exists in different states (the naked DNA or thein vitro reconstituted nucleosomal DNA) are quite different. We speculate that HMG proteins might play a critical role in the regulation of the human β-like globin gene’s expression.
Analysis of nucleosome positioning in promoters of miRNA genes and protein-coding genes
HongDe Liu,DeJin Zhang,JianMing Xie,ZhiDong Yuan,Xin Ma,ZhiYuan Lu,LeJun Gong,Xiaoauthor Sun
Chinese Science Bulletin , 2010, DOI: 10.1007/s11434-009-3730-2
Abstract: Nucleosome positioning in promoters is important for gene transcription regulation. In this paper, with a nucleosome prediction model, curvature profile, the characteristics of nucleosome positioning in promoters are analyzed for miRNA genes and protein-coding genes. In the vicinity of transcription start site (TSS), there is a nucleosome-free region (NFR) followed by a positioned nucleosome at ~200 bp downstream of TSS. A similar characteristic is observed in independent intronic promoters and intergenic promoters, namely, both types of promoters have a longer NFR in 0– 400 bp upstream of TSS. Moreover, transcription factor binding sites (TFBSs) locate in the NFR with a high concentration. However, nucleosome pattern in dependent intronic promoters are like that in protein-coding promoters, with two nucleosomes positioned at 200– 400 bp and 400– 600 bp upstream of TSS. The results indicate nucleosome positioning is probably different in independent miRNA promoters and protein-coding promoters; and positioning seems to be an important factor not only in regulation of protein-coding gene, but also in that of miRNA gene.
A New Histone Structure Which Binds DNA at Its Eight Subunit N-Termini  [PDF]
Ken Biegeleisen
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1102386
Abstract: A new model for the nucleosome is presented. The histone octamer core is unchanged, but the location of the DNA is different. Since the highest number, and highest concentration of positively- charged amino acid residues is located not in the “superhelical ramp” of the octamer core, but rather in the domain of the eight histone subunit N-termini collectively, the DNA is therefore placed there. The role models for the protein and DNA structures in the N-terminal domain are taken from the comparable role models for protein and DNA in the protamine-DNA complex in sperm cells. The histone subunit N-termini are each modeled as beta-strands, with psi/phi values of approximately /﹣130.5° respectively, which gives a straight chain. The DNA is modeled according to the “straight ladder” model of Tai Te Wu. Each DNA phosphate group is bound to a lysine or arginine residue of histone by a 3 A salt bridge. The new model lends itself so readily to further models of higher-order chromatin structure that the problem shifts entirely, from one of deducing any higher-order structure at all, to one of distinguishing between several models which compete for our attention.
Statistical analysis of conformational properties of periodic dinucleotide steps in nucleosomes  [PDF]
Xi Yang, Hong Ya
Journal of Biomedical Science and Engineering (JBiSE) , 2010, DOI: 10.4236/jbise.2010.34046
Abstract: Deformability of DNA is important for its superhelical folding in the nucleosome and has long been thought to be facilitated by periodic occurrences of certain dinucleotides along the sequences, with the period close to 10.5 bases. This study statistically examines the conformational properties of dinucleotides containing the 10.5 - base periodicity and those without that periodicity through scanning all nucleosome structures provided in PDB. By categorizing performances on the distribution of step parameter values, averaged net values, standard deviations and deformability based on step conformational energies, we give a detailed description as to the deformation preferences correlated with the periodicity for the 10 unique types of dinucleotides and summarize the possible roles of various steps in how they facilitate DNA bending. The results show that the structural properties of dinucleotide steps are influenced to various extents by the periodicity in nucleosomes and some periodic steps have shown a clear tendency to take specific bending or shearing patterns.
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