An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

Marathe, Arvind; Bansal, Manju
January 2011
BMC Structural Biology;2011, Vol. 11 Issue 1, p1
Academic Journal
Background: A nucleosome is the fundamental repeating unit of the eukaryotic chromosome. It has been shown that the positioning of a majority of nucleosomes is primarily controlled by factors other than the intrinsic preference of the DNA sequence. One of the key questions in this context is the role, if any, that can be played by the variability of nucleosomal DNA structure. Results: In this study, we have addressed this question by analysing the variability at the dinucleotide and trinucleotide as well as longer length scales in a dataset of nucleosome X-ray crystal structures. We observe that the nucleosome structure displays remarkable local level structural versatility within the B-DNA family. The nucleosomal DNA also incorporates a large number of kinks. Conclusions: Based on our results, we propose that the local and global level versatility of B-DNA structure may be a significant factor modulating the formation of nucleosomes in the vicinity of high-plasticity genes, and in varying the probability of binding by regulatory proteins. Hence, these factors should be incorporated in the prediction algorithms and there may not be a unique 'template' for predicting putative nucleosome sequences. In addition, the multimodal distribution of dinucleotide parameters for some steps and the presence of a large number of kinks in the nucleosomal DNA structure indicate that the linear elastic model, used by several algorithms to predict the energetic cost of nucleosome formation, may lead to incorrect results.


Related Articles

  • In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice. Motohiro Mihara; Takeshi Itoh; Takeshi Izawa // Plant & Cell Physiology;Oct2008, Vol. 49 Issue 10, p1451 

    Microarray analysis of tiny amounts of RNA extracted from plant section samples prepared by laser microdissection (LM) can provide high-quality information on gene expression in specified plant cells at various stages of development. Having joined the LM-microarray analysis project, we utilized...

  • Organisation du génome embryonnaire après la fécondation chez les mammifères. Beaujean, Nathalie; Mason, Karlia; Bonnet-Gamier, Amélie; Salvaing, Juliette; Debey, Pascale // Biologie Aujourd'hui;2010, Vol. 204 Issue 3, p205 

    No abstract available.

  • Statistical challenges associated with detecting copy number variations with next-generation sequencing. Teo, Shu Mei; Pawitan, Yudi; Ku, Chee Seng; Chia, Kee Seng; Salim, Agus // Bioinformatics;Nov2012, Vol. 28 Issue 21, p2711 

    Motivation: Analysing next-generation sequencing (NGS) data for copy number variations (CNVs) detection is a relatively new and challenging field, with no accepted standard protocols or quality control measures so far. There are by now several algorithms developed for each of the four broad...

  • RNA sequencing potent tool for understanding gene expression.  // Australian Life Scientist;3/11/2010, p1 

    Two studies in Nature show the power of RNA sequencing in exploring the genetic mechanisms that underpin gene expression.

  • Characterization of regulatory features of housekeeping and tissue-specific regulators within tissue regulatory networks. Pengping Li; Xu Hua; Zhen Zhang; Jie Li; Jin Wang // BMC Systems Biology;2013, Vol. 7 Issue 1, p2 

    Background Transcription factors (TFs) and miRNAs are essential for the regulation of gene expression; however, the global view of human gene regulatory networks remains poorly understood. For example, how is the expression of so many genes regulated by limited cohorts of regulators and how are...

  • A Target Site for Spontaneous Insertion of IS10 Element in pUC19 DNA Located within Intrinsically Bent DNA. Shungo Kobori; Yumi Ko; Mikio Kato // Open Microbiology Journal;2009, Vol. 3, p146 

    Residual insertion sequence elements (IS elements) in Escherichia coli strains that are commonly used for DNA cloning are known to cause cloning artifacts by transposing themselves into the recombinant DNA fragments. In such cases, chance insertion of IS elements may occur at integration sites...

  • PrimerIdent: A web based tool for conserved primer design. Pessoa, Alberto M.; Pereira, Susana; Teixeira, Jorge // Bioinformation;2010, Vol. 5 Issue 2, p52 

    Conserved primers across multiple species and simultaneously specific for a certain isozyme can be rare and difficult to find. PrimerIdent was developed aiming to automate this primer design and selection process in a given nucleotide sequence alignment, providing an intuitive, easy to interpret...

  • The functional landscape of mouse gene expression. Wen Zhang; Morris, Quaid D.; Chang, Richard; Shai, Ofer; Bakowski, Malina A.; Mitsakakis, Nicholas; Mohammad, Naveed; Robinson, Mark D.; Zirngibl, Ralph; Somogyi, Eszter; Laurin, Nancy; Eftekharpour, Eftekhar; Sat, Eric; Grigull, Jörg; Qun Pan; Wen-Tao Peng; Krogan, Nevan; Greenblatt, Jack; Fehlings, Michael; Van der Kooy, Derek // Journal of Biology;2004, Vol. 3, p21 

    Background: Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-specific expression is indicative...

  • Spatial regulation dominates gene function in the ganglia chain. Hibsh, Dror; Schori, Hadas; Efroni, Sol; Shefi, Orit // Bioinformatics;Feb2014, Vol. 30 Issue 3, p310 

    Motivation: To understand the molecular mechanisms of neurons, it is imperative to identify genomic dissimilarities within the heterogeneity of the neural system. This is especially true for neuronal disorders in which spatial considerations are of critical nature. For this purpose, Hirudo...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics