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

Author

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

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.

Suggested Citation

  • 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, Elsevier, vol. 366(C), pages 308-322.
    • Handle: RePEc:eee:phsmap:v:366:y:2006:i:c:p:308-322
    DOI: 10.1016/j.physa.2005.10.019
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    References listed on IDEAS

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    1. Provata, A. & Almirantis, Y., 1997. "Scaling properties of coding and non-coding DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 247(1), pages 482-496.
    2. Hao, Bai-Lin, 2000. "Fractals from genomes – exact solutions of a biology-inspired problem," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 282(1), pages 225-246.
    3. Provata, A., 1999. "Random aggregation models for the formation and evolution of coding and non-coding DNA," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 264(3), pages 570-580.
    4. Katsaloulis, P & Theoharis, T & Provata, A, 2002. "Statistical distributions of oligonucleotide combinations: applications in human chromosomes 21 and 22," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 316(1), pages 380-396.
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    Cited by:

    1. Silva, R. & Silva, J.R.P. & Anselmo, D.H.A.L. & Alcaniz, J.S. & da Silva, W.J.C. & Costa, M.O., 2020. "An alternative description of power law correlations in DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 545(C).
    2. Wu, Zuo-Bing, 2010. "Global transposable characteristics in the complete DNA sequence of the yeast," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(24), pages 5698-5705.
    3. Moghaddasi, Hanieh & Rezaei, Soghra & Darooneh, Amir Hossein & Heshmati, Emran & Khalifeh, Khosrow, 2020. "A comparative analysis of dipeptides distribution in eukaryotes and prokaryotes by statistical mechanics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 555(C).
    4. Craciun, Dana & Isvoran, Adriana & Avram, N.M., 2009. "Long range correlation of hydrophilicity and flexibility along the calcium binding protein chains," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 388(21), pages 4609-4618.

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