Statistical analysis of DNA sequences containing nucleosome positioning sites

Computer prediction of nucleosome positioning sites from DNA sequences is of great importance for analyzing eukaryotic gene expression regulation. Investigation of experimentally found nucleosome positioning sites determined statistically significant contexts and revealed symmetry of their distribut...

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Bibliographic Details
Published in:Biophysics (Oxford) 2006-08, Vol.51 (4), p.541-546
Main Authors: Orlov, Yu L, Levitskii, V G, Smirnova, O G, Podkolodnaya, O A, Khlebodarova, T M, Kolchanov, N A
Format: Article
Language:English
Subjects:
Binding sites
Cytology
Deoxyribonucleic acid
DNA
Eukaryotes
Exons
Gene expression
Gene regulation
Introns
Markov chains
Nucleotide sequence
Promoters
Statistical analysis
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Summary:Computer prediction of nucleosome positioning sites from DNA sequences is of great importance for analyzing eukaryotic gene expression regulation. Investigation of experimentally found nucleosome positioning sites determined statistically significant contexts and revealed symmetry of their distribution about the center of a site. Internet-available software was developed to determine the profile of preference of genomic DNA for nucleosome formation (nucleosome potential) on the basis of Markov models. A correlation of the nucleosome potential with the complexity of the nucleotide sequence text was established. The nucleosome potential was estimated for transcription factor binding sites, promoters, exons, and introns of eukaryotic genes. A difference in nucleosome potential between promoters of tissue-specific and constitutively expressed eukaryotic genes was shown. The software is available at the website of the Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences at th address http://www.mgs.bionet.nsc.ru/programs/VMM/.
ISSN:0006-3509
1555-6654
DOI:10.1134/S0006350906040051