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Biophysics

, 56:114 | Cite as

Preferred distances between transcription factor binding sites

  • I. V. Kulakovskiy
  • A. S. Kasianov
  • A. A. Belostotsky
  • I. A. Eliseeva
  • V. J. Makeev
Letters to the Editor

Abstract

Transcriptional regulation of gene expression in higher eukaryotes is driven by elaborate protein complexes of transcription factors. At the DNA level, these complexes interact with composite elements consisting of specific binding sites for different proteins. We use the hypoxia-response system to identify preferred localization distances between “hypoxia-induced factor-1 — cofactor” binding site pairs in promoter DNA regions of the human genome. Such characteristic co-localization distances agree with a supposed scale of regulatory regions while being significantly longer than the typical binding site length. We speculate that this phenomenon can provide a key to decipher the structure of DNA regulatory regions in higher eukaryotes.

Keywords

transcription factor binding sites co-localization hypoxia Homo sapiens 

References

  1. 1.
    R. H. Wenger, D. P. Stiehl, and G. Camenisch, Sci. STKE, 306, re12 (2005).CrossRefGoogle Scholar
  2. 2.
    H. I. Swanson, W. K. Chan, and C. A. Bradfield, J. Biol. Chem. 270, 26292 (1995).CrossRefGoogle Scholar
  3. 3.
    V. Matys, O. V. Kel-Margoulis, E. Fricke, et al., Nucleic Acids Res. 34, D108 (2006).CrossRefGoogle Scholar
  4. 4.
    K. D. Yokoyama, U. Ohler, and G. A. Wray, Nucleic Acids Res. 37, e92 (2009).CrossRefGoogle Scholar
  5. 5.
    T. Sanchez-Elsner, J. R. Ramirez, F. Sanz-Rodriguez, et al., J. Mol. Biol. 336, 9 (2004).CrossRefGoogle Scholar
  6. 6.
    A. Ortiz-Barahona, D. Villar, N. Pescador, et al., Nucleic Acids Res. 38, 2332 (2010).CrossRefGoogle Scholar
  7. 7.
    X. Xia, M. E. Lemieux, W. Li, et al., Proc. Natl. Acad. Sci. USA 106, 4260 (2009).ADSCrossRefGoogle Scholar
  8. 8.
    I. V. Kulakovskiy and V. J. Makeev, Biophysics 54, 667 (2009).CrossRefGoogle Scholar
  9. 9.
    I. V. Kulakovskiy, A. V. Favorov, and V. J. Makeev, Bioinformatics 25, 2318 (2009).CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2011

Authors and Affiliations

  • I. V. Kulakovskiy
    • 1
    • 2
  • A. S. Kasianov
    • 1
  • A. A. Belostotsky
    • 2
  • I. A. Eliseeva
    • 3
  • V. J. Makeev
    • 2
  1. 1.Engelhardt Institute of Molecular BiologyRussian Academy of SciencesMoscowRussia
  2. 2.Research Institute for Genetics and Selection of Industrial MicroorganismsMoscowRussia
  3. 3.Institute for Protein ResearchRussian Academy of SciencesPushchinoRussia

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