Sequence periodicity in nucleosomal DNA and intrinsic curvature

Nair, T. Murlidharan
January 2010
BMC Structural Biology;2010 Supplement 1, Vol. 10, Special section p1
Academic Journal
Background: Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Results: Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. Conclusions: The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA.


Related Articles

  • SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Matsumura, Hideo; Nasir, Khairun Hisam Bin; Yoshida, Kentaro; Ito, Akiko; Kahl, Günter; Krüger, Detlev H.; Terauchi, Ryohei // Nature Methods;Jun2006, Vol. 3 Issue 6, p469 

    We developed a new platform for genome-wide gene expression analysis in any eukaryotic organism, which we called SuperSAGE array. The SuperSAGE array is a microarray onto which 26-bp oligonucleotides corresponding to SuperSAGE tag sequences are directly synthesized. A SuperSAGE array combines...

  • The effect of sequencing errors on metagenomic gene prediction. Hoff, Katharina J. // BMC Genomics;2009, Vol. 10, p520 

    Background: Gene prediction is an essential step in the annotation of metagenomic sequencing reads. Since most metagenomic reads cannot be assembled into long contigs, specialized statistical gene prediction tools have been developed for short and anonymous DNA fragments, e.g. MetaGeneAnnotator...

  • Search for somatic DNA variation in the brain: investigation of the serotonin 2A receptor gene. Kaminsky, Zachary A.; Popendikyte, Violeta; Assadzadeh, Abbas; Petronis, Arturas // Mammalian Genome;Aug2005, Vol. 16 Issue 8, p587 

    Somatic DNA variation represents one of the most interesting but also one of the least investigated genetic phenomena. In addition to the classical case of DNA hypermutability at the V(D)J region, there is an increasing body of experimental evidence suggesting that genes other than...

  • A variety of synergistic and antagonistic interactions mediated by cis-acting DNA motifs regulate gene expression in plant cells and modulate stability of the transcription complex formed on a basal promoter. Sawant, Samir V.; Kiran, Kanti; Mehrotra, Rajesh; Chaturvedi, Chandra Prakash; Ansari, Suraiya A.; Singh, Pratibha; Lodhi, Niraj; Tuli, Rakesh // Journal of Experimental Botany;Sep2005, Vol. 56 Issue 419, p2345 

    Several synthetic promoters containing a variety of commonly found cis-acting DNA sequence motifs were constructed to study the motif–motif and motif–protein interactions involved in gene expression in plants. Transient expression of the reporter gene gusA in tobacco leaves was...

  • Statistical methods for detecting periodic fragments in DNA sequence data.  // Biology Direct;2011, Vol. 6 Issue 1, p21 

    The article offers information on a study conducted by researchers to detect periodic fragments in DNA sequence data. It states that DNA's ability to produce nucleosomes is influenced by period 10 dinucleotides. It also mentions about the relevance of Hybrid estimation method in the analysis of...

  • Multiple nuclear pseudogenes of mitochondrial DNA exist in the canine genome. Ishiguro, Naotaka; Nakajima, Ayako; Horiuchi, Motohiro; Shinagawa, Morikazu // Mammalian Genome;Jul2002, Vol. 13 Issue 7, p365 

    Many copies of nuclear counterparts of mitochondrial DNA (mtDNA) were found in nuclear DNA from sperm heads of the domestic dog, Canis familiaris, by DNA-DNA hybridization and DNA sequencing. Nuclear counterparts homologous to the mtDNA D-loop region were cloned into l phage vectors (EMBL4 and...

  • Rationally designed insulator-like elements can block enhancer action in vitro. V.A. Bondarenko; Y.I. Jiang; V.M. Studitsky // EMBO Journal;9/15/2003, Vol. 22 Issue 18, p4728 

    Insulators are DNA sequences that are likely to be involved in formation of chromatin domains, functional units of gene expression in eukaryotes. Insulators can form domain boundaries and block inappropriate action of regulatory elements (such as transcriptional enhancers) in eukaryotic nuclei....

  • Recombination within mouse t haplotypes has replaced significant segments of t-specific DNA. Wallace, Lyle T.; Erhart, Mark A. // Mammalian Genome;Apr2008, Vol. 19 Issue 4, p263 

    Previous studies on the fourth inversion of the t complex, In17(4), suggest that loci near the center of this inversion have been subjected to segmental recombination during the past 1�2 million years. We have used a combination of PCR-based restriction site (PBR) analysis and DNA...

  • Understanding Human DNA Sequence Variation. Kidd, K. K.; Pakstis, A. J.; Speed, W. C.; Kidd, J. R.; Holsinger, Kent E. // Journal of Heredity;Sep/Oct2004, Vol. 95 Issue 5, p406 

    Over the past century researchers have identified normal genetic variation and studied that variation in diverse human populations to determine the amounts and distributions of that variation. That information is being used to develop an understanding of the demographic histories of the...


Read the Article


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

Try another library?
Sign out of this library

Other Topics