Long-range correlations of RNA polymerase II promoter sequences across organisms

P. Katsaloulis, T. Theoharis, W. M. Zheng, B. L. Hao, A. Bountis, Y. Almirantis, A. Provata

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

The statistical properties of the size distribution of DNA segments separating identical oligonucleotides are studied. For representative eukaryotes (Homo sapiens, Mus musculus, Saccharomyces cereviciae, Oryza sativa, Arabidopsis thaliana) we have demonstrated the existence of long-range correlations for the distances separating oligonucleotides of sizes 4, 5 and 6, which carry a promoter signature. This observation is independent of the consensus sequence used by the organism, as in the case of O. sativa (which mainly uses the CG promoter box) and A. thaliana (which mainly uses the TATA promoter box). If we use two parameters to characterise the size distribution separating oligonucleotides, we observe that oligonucleotides containing promoter signatures cluster together, away from the others.

Original languageEnglish
Pages (from-to)308-322
Number of pages15
JournalPhysica A: Statistical Mechanics and its Applications
Volume366
DOIs
Publication statusPublished - Jul 1 2006
Externally publishedYes

Fingerprint

Long-range Correlations
oligonucleotides
organisms
Promoter
Oryza Sativa
Arabidopsis Thaliana
boxes
Signature
signatures
eukaryotes
saccharomyces
Statistical property
Two Parameters
deoxyribonucleic acid

Keywords

  • Consensus sequences
  • Critical exponents
  • Long-range correlations
  • Oligonucleotide size distribution
  • Promoters

ASJC Scopus subject areas

  • Mathematical Physics
  • Statistical and Nonlinear Physics

Cite this

Katsaloulis, P., Theoharis, T., Zheng, W. M., Hao, B. L., Bountis, A., Almirantis, Y., & Provata, A. (2006). Long-range correlations of RNA polymerase II promoter sequences across organisms. Physica A: Statistical Mechanics and its Applications, 366, 308-322. https://doi.org/10.1016/j.physa.2005.10.019

Long-range correlations of RNA polymerase II promoter sequences across organisms. / Katsaloulis, P.; Theoharis, T.; Zheng, W. M.; Hao, B. L.; Bountis, A.; Almirantis, Y.; Provata, A.

In: Physica A: Statistical Mechanics and its Applications, Vol. 366, 01.07.2006, p. 308-322.

Research output: Contribution to journalArticle

Katsaloulis, P, Theoharis, T, Zheng, WM, Hao, BL, Bountis, A, Almirantis, Y & Provata, A 2006, 'Long-range correlations of RNA polymerase II promoter sequences across organisms', Physica A: Statistical Mechanics and its Applications, vol. 366, pp. 308-322. https://doi.org/10.1016/j.physa.2005.10.019
Katsaloulis, P. ; Theoharis, T. ; Zheng, W. M. ; Hao, B. L. ; Bountis, A. ; Almirantis, Y. ; Provata, A. / Long-range correlations of RNA polymerase II promoter sequences across organisms. In: Physica A: Statistical Mechanics and its Applications. 2006 ; Vol. 366. pp. 308-322.
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