Abstract
BackgroundMost 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.ResultsHigher 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.ConclusionsThe 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.
Highlights
Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers
With a view to understand how this periodicity of certain dinucleotides translates into intrinsic deformability, the sequence-directed structures associated with the nucleosome DNA of C. elegans and chicken nucleosome have been analyzed using the theoretical models for DNA curvature
Recent analysis by measuring the distance between YY, YR, RR and RY dinucleotides of nucleosome DNA fragments from C. elegans revealed a consensus sequence structure of the nucleosome DNA repeat to be (YYYYYRRRRR)n [20]
Summary
Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. The higher the stacking energy the more rigid the DNA helix, it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Eukaryotic chromosome consists of a single DNA molecule that has been compacted several thousand fold by interacting with highly conserved proteins called core histones. The nucleosome core is made up of 146 bp of negatively charged DNA wrapped 1.65 times around highly basic proteins called histones, which neutralizes the negative charge. The formation of the chromatin facilitates the packaging of DNA into chromosomes by compacting it several thousand folds. Recent studies have thrown light into the basic organization of nucleosomes on chromosomes and their role in regulating genomic function (reviewed in [4])
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