oalib

OALib Journal期刊

ISSN: 2333-9721

费用:99美元

投稿

匹配条件: “ Nucleosome” ,找到相关结果约34条。
列表显示的所有文章,均可免费获取
第1页/共34条
每页显示
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.
The Emerging Roles of ATP-Dependent Chromatin Remodeling Enzymes in Nucleotide Excision Repair
Wioletta Czaja,Peng Mao,Michael J. Smerdon
International Journal of Molecular Sciences , 2012, DOI: 10.3390/ijms130911954
Abstract: DNA repair in eukaryotic cells takes place in the context of chromatin, where DNA, including damaged DNA, is tightly packed into nucleosomes and higher order chromatin structures. Chromatin intrinsically restricts accessibility of DNA repair proteins to the damaged DNA and impacts upon the overall rate of DNA repair. Chromatin is highly responsive to DNA damage and undergoes specific remodeling to facilitate DNA repair. How damaged DNA is accessed, repaired and restored to the original chromatin state, and how chromatin remodeling coordinates these processes in vivo, remains largely unknown. ATP-dependent chromatin remodelers (ACRs) are the master regulators of chromatin structure and dynamics. Conserved from yeast to humans, ACRs utilize the energy of ATP to reorganize packing of chromatin and control DNA accessibility by sliding, ejecting or restructuring nucleosomes. Several studies have demonstrated that ATP-dependent remodeling activity of ACRs plays important roles in coordination of spatio-temporal steps of different DNA repair pathways in chromatin. This review focuses on the role of ACRs in regulation of various aspects of nucleotide excision repair (NER) in the context of chromatin. We discuss current understanding of ATP-dependent chromatin remodeling by various subfamilies of remodelers and regulation of the NER pathway in vivo.
Roles of histones and nucleosomes in gene transcription
Baiqu Huang,Qinhua Zeng,Xiaohui Bi,Yuhong Wang,Yuxin Li
Chinese Science Bulletin , 2001, DOI: 10.1007/BF03187162
Abstract: This article reviews the latest research developments in the field of eukaryotic gene regulation by the structural alterations of chromatin and nucleosomes. The following issues are briefly addressed: (i) nucleosome and histone modifications by both the ATP-dependent remodeling complexes and the histone acetyltransferases and their roles in gene activation; (ii) competitive binding of histones and transcription factors on gene promoters, and transcription repression by nucleosomes; and (iii) influences of linker histone H1 on gene regulation. Meanwhile, the significance and impact of these new research progresses, as well as issues worthwhile for further study are commented.
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.
Nucleosome conformational flexibility in experiments with single chromatin fibers
Sivolob A. V.
Biopolymers and Cell , 2010,
Abstract: Studies on the chromatin nucleosome organization play an ever increasing role in our comprehension of mechanisms of the gene activity regulation. This minireview describes the results on the nucleosome conformational flexibility, which were obtained using magnetic tweezers to apply torsion to oligonucleosome fibers reconstituted on single DNA molecules. Such an approach revealed a new structural form of the nucleosome, the reversome, in which DNA is wrapped in a right-handed superhelix around a distorted histone octamer. Molecular mechanisms of the nucleosome structural flexibility and its biological relevance are discussed.
Chromatin Fiber Dynamics under Tension and Torsion
Christophe Lavelle,Jean-Marc Victor,Jordanka Zlatanova
International Journal of Molecular Sciences , 2010, DOI: 10.3390/ijms11041557
Abstract: Genetic and epigenetic information in eukaryotic cells is carried on chromosomes, basically consisting of large compact supercoiled chromatin fibers. Micromanipulations have recently led to great advances in the knowledge of the complex mechanisms underlying the regulation of DNA transaction events by nucleosome and chromatin structural changes. Indeed, magnetic and optical tweezers have allowed opportunities to handle single nucleosomal particles or nucleosomal arrays and measure their response to forces and torques, mimicking the molecular constraints imposed in vivo by various molecular motors acting on the DNA. These challenging technical approaches provide us with deeper understanding of the way chromatin dynamically packages our genome and participates in the regulation of cellular metabolism.
The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner
Frank Sleutels, Widia Soochit, Marek Bartkuhn, Helen Heath, Sven Dienstbach, Philipp Bergmaier, Vedran Franke, Manuel Rosa-Garrido, Suzanne van de Nobelen, Lisa Caesar, Michael van der Reijden, Jan Bryne, Wilfred van IJcken, J Grootegoed, M Delgado, Boris Lenhard, Rainer Renkawitz, Frank Grosveld, Niels Galjart
Epigenetics & Chromatin , 2012, DOI: 10.1186/1756-8935-5-8
Abstract: Using immunohistochemistry on testis sections and fluorescence-based microscopy on intact live seminiferous tubules, we show that CTCFL is only transiently present during spermatogenesis, prior to the onset of meiosis, when the protein co-localizes in nuclei with ubiquitously expressed CTCF. CTCFL distribution overlaps completely with that of Stra8, a retinoic acid-inducible protein essential for the propagation of meiosis. We find that absence of CTCFL in mice causes sub-fertility because of a partially penetrant testicular atrophy. CTCFL deficiency affects the expression of a number of testis-specific genes, including Gal3st1 and Prss50. Combined, these data indicate that CTCFL has a unique role in spermatogenesis. Genome-wide RNA expression studies in ES cells expressing a V5- and GFP-tagged form of CTCFL show that genes that are downregulated in CTCFL-deficient testis are upregulated in ES cells. These data indicate that CTCFL is a male germ cell gene regulator. Furthermore, genome-wide DNA-binding analysis shows that CTCFL binds a consensus sequence that is very similar to that of CTCF. However, only ~3,700 out of the ~5,700 CTCFL- and ~31,000 CTCF-binding sites overlap. CTCFL binds promoters with loosely assembled nucleosomes, whereas CTCF favors consensus sites surrounded by phased nucleosomes. Finally, an ES cell-based rescue assay shows that CTCFL is functionally different from CTCF.Our data suggest that nucleosome composition specifies the genome-wide binding of CTCFL and CTCF. We propose that the transient expression of CTCFL in spermatogonia and preleptotene spermatocytes serves to occupy a subset of promoters and maintain the expression of male germ cell genes.Three-dimensional folding of the eukaryotic genome occurs in a highly organized manner so as to compact chromatin while allowing temporal and spatial expression of genes. The genome contains regulatory elements, such as promoters, enhancers, locus control regions, insulators and enhancer blockers,
Functions of chromatin remodeling factors in heterochromatin formation and maintenance
Xin Bi
Science China Life Sciences , 2012, DOI: 10.1007/s11427-012-4267-1
Abstract: Heterochromatin is characteristically more compact than euchromatin in the eukaryotic genome. The establishment of heterochromatin is mediated by special histone modifications, recruitment and propagation of heterochromatin specific proteins, as well as formation of special primary and high order structures of chromatin. Chromatin remodeling factors are ATPases that can alter the conformation and/or positioning of nucleosomes along DNA in an ATP-dependent manner. There is increasing evidence implicating chromatin remodeling activities in heterochromatin in various organisms ranging from yeasts to humans. Chromatin remodeling factors play roles in the establishment, maintenance and epigenetic inheritance of heterochromatin, but the underlying molecular mechanisms have just begun to be investigated.
第1页/共34条
每页显示


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.