Article

Search of regular sequences in promoters from eukaryotic genomes

Bioengineering Centre of Russian Academy of Sciences, 117312 Moscow, Pr-t 60-tya Oktyabrya, 7/1, Russian Federation.
Computational biology and chemistry (Impact Factor: 1.6). 04/2009; 33(3):196-204. DOI: 10.1016/j.compbiolchem.2009.03.001
Source: PubMed

ABSTRACT In this paper, the notion of "regularity" is introduced to describe the structural features of DNA sequences. This notion expands the "latent periodicity" term. The novel method for revealing regularity based on the runs test is described. The search of regular sequences in eukaryotic promoters has shown that more than 60% of them possess a regularity property on statistically significant level. Possible biological functions of regularity are discussed together with the possibility of using this characteristic for performing promoter annotation.

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Available from: Eugene V Korotkov, Aug 31, 2015
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    • "It was also found that fuzzy periodicity with a period length about 10–12 nucleotides was present in promoter sequences. Such periodicity may correspond to DNA bend near promoter region (Shelenkov and Korotkov, 2009). Further development of the information decomposition method was aimed to improve detection of fuzzy periodicity containing indels. "
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    ABSTRACT: We describe a new mathematical method for finding very diverged short tandem repeats containing a single indel. The method involves comparison of two frequency matrices: a first matrix for a subsequence before shift and a second one for a subsequence after it. A measure of comparison is based on matrix similarity. The approach developed was applied to analysis of the genomes of Caenorhabditis elegans, Drosophila melanogaster and Saccharomyces cerevisiae. They were investigated regarding the presence of tandem repeats having repeat length equal to 2 - 11 nucleotides except equal to 3, 6 and 9 nucleotides. A number of phase shift regions for these genomes was approximately 2.2×10(4), 1.5×10(4) and 1.7×10(2), respectively. Type I error was less than 5%. The mean length of fuzzy periodicity and phase shift regions was about 220 nucleotides. The regions of fuzzy periodicity having single insertion or deletion occupy substantial parts of the genomes: 5%, 3% and 0.3%, respectively. Only less than 10% of these regions have been detected previously. That is, the number of such regions in the genomes of C. elegans, D. melanogaster and S. cerevisiae is dramatically higher than it has been revealed by any known methods. We suppose that some found regions of fuzzy periodicity could be the regions for protein binding.
    Computational biology and chemistry 04/2014; 51C:12-21. DOI:10.1016/j.compbiolchem.2014.03.004 · 1.60 Impact Factor
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    • "It was also found that fuzzy periodicity with a period length about 10–12 nucleotides was present in promoter sequences. Such periodicity may correspond to DNA bend near promoter region (Shelenkov and Korotkov, 2009). Further development of the information decomposition method was aimed to improve detection of fuzzy periodicity containing indels. "
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    • "In particular, the static DNA curvature upstream of the transcription start has been shown to modulate transcription [1] [2] [3] [4]. Since DNA curvature is related to A/T tracts phased with the pitch of the double helix, the study of A/T patterns with periods 10–11 bp can provide essential information on the regulatory mechanisms [5] [6] [7] [8] [9]. In accordance with their regulatory functions, A/T patterns with the helix period tend to concentrate in the intergenic regions [10]. "
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