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Biophysics

, Volume 62, Issue 6, pp 857–864 | Cite as

The Physical and Geometric Properties of Human Transposon Stem–Loop Structures under Natural Selection

  • D. A. GrechishnikovaEmail author
  • M. S. Poptsova
Molecular Biophysics
  • 16 Downloads

Abstract

Secondary RNA structures play an important role in transposition, in particular, in RNA recognition by transposon proteins. Previously, we found a conserved structure at the 3′-end of human transposons and proposed a hypothesis about the role of this structure in transposition. Although there is no similarity at the sequence level, the conserved position of this structure points to the fact that structural properties occur that are under positive natural selection. In this paper, the physical and geometric properties of stem-loop structures at the 3′-end of human transposons are identified and compared with properties of the structures of other genome regions. Each stem-loop structure was characterized by a set of ten characteristics: the Gibbs free energy, enthalpy, entropy, hydrophilicity, Shift, Slide, Rise, Tilt, Roll, and Twist. A model has been built using machine-learning methods, which recognizes stem-loop structures according to their physical and geometric characteristics with 94% accuracy. The most important parameters in the recognition model are hydrophilicity, enthalpy, Rise, and Twist. These properties of transposon structure are thought to be under positive natural selection.

Keywords

transposon stem-loop structure dinucleotide characteristics entropy Gibbs free energy machine learning 

Abbreviation

LINE

long interspersed elements

SINE

short interspersed elements

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References

  1. 1.
    C. R. Huang, K. H. Burns, and J. D. Boeke, Annu. Rev. Genet. 46, 651 (2012).CrossRefGoogle Scholar
  2. 2.
    E. S. Lander, et al., Nature 409 (6822), 860 (2001).ADSCrossRefGoogle Scholar
  3. 3.
    D. C. Hancks and H. H. Kazazian, Jr., Curr. Opin. Genet. Dev. 22 (3), 191 (2012).CrossRefGoogle Scholar
  4. 4.
    C. R. Beck, et al., Annu. Rev. Genomics Hum. Genet. 12, 187 (2011).CrossRefGoogle Scholar
  5. 5.
    H. H. Kazazian, Jr., Science 303 (5664), 1626 (2004).ADSCrossRefGoogle Scholar
  6. 6.
    S. R. Richardson, et al., Microbiol. Spectr. 3 (2), MDNA3-0061-2014 (2015).Google Scholar
  7. 7.
    Y. Hayashi, et al., Nucleic Acids Res. 42 (16), 10605 (2014).CrossRefGoogle Scholar
  8. 8.
    M. Kajikawa and N. Okada, Cell 111 (3), 433 (2002).CrossRefGoogle Scholar
  9. 9.
    Osanai, M., et al., Mol. Cell Biol. 24 (18), 7902 (2004).CrossRefGoogle Scholar
  10. 10.
    D. Grechishnikova and M. Poptsova, BMC Genomics 17 (1), 992 (2016).CrossRefGoogle Scholar
  11. 11.
    N. M. Luscombe, et al., Genome Biol. 1 (1), REVIEWS001 (2000).Google Scholar
  12. 12.
    P. Barraud and F. H. Allain, Curr. Top. Microbiol. Immunol. 353, 35 (2012).Google Scholar
  13. 13.
    W. Chen, et al., Sci. Rep. 6, 35123 (2016).ADSCrossRefGoogle Scholar
  14. 14.
    W. Chen, et al., Nucleic Acids Res. 41 (6), e68 (2013).CrossRefGoogle Scholar
  15. 15.
    W. Chen, et al., Biomed. Res. Int. 2014, 623149 (2014).Google Scholar
  16. 16.
    B. Liu, F. Yang, and K. C. Chou, Mol. Ther. Nucleic Acids 7, 267 (2017).CrossRefGoogle Scholar
  17. 17.
    M. Friedel, S. Nikolaiewa, J. Sühnel, and T. Wilhelm, Nucleic Acids Res. 37 (Database issue), D37 (2009).CrossRefGoogle Scholar
  18. 18.
    X. J. Lu and W. K. Olson, Nucleic Acids Res. 31 (17), 5108 (2003).CrossRefGoogle Scholar
  19. 19.
    C. O. Pabo and R. T. Sauer, Annu. Rev. Biochem. 53, 293 (1984).CrossRefGoogle Scholar
  20. 20.
    P. C. van der Vliet and C. P. Verrijzer, Bioessays 15 (1), 25 (1993).CrossRefGoogle Scholar
  21. 21.
    R. E. Dickerson, Nucleic Acids Res. 26 (8), 1906 (1998).CrossRefGoogle Scholar
  22. 22.
    V. A. Tverdislov, Biophysics (Moscow) 58 (1), 128 (2013).CrossRefGoogle Scholar
  23. 23.
    G. Masliah, P. Barraud, and F. H. Allain, Cell. Mol. Life Sci. 70 (11), 1875 (2013).Google Scholar
  24. 24.
    R. Stefl, L. Skrisovska, and F. H. Allain, EMBO Rep. 6 (1), 33 (2005).CrossRefGoogle Scholar
  25. 25.
    J. R. Williamson, Nat. Struct. Biol. 7 (10), 834 (2000).CrossRefGoogle Scholar
  26. 26.
    J. M. Thomas and P. A. Beal, BioEssays 39 (4), 1600187 (2017).CrossRefGoogle Scholar
  27. 27.
    R. Thapar, A. P. Denmon, and E. P. Nikonowicz, Wiley Interdiscip. Rev. RNA 5 (1), 49 (2014).CrossRefGoogle Scholar
  28. 28.
    K. Wild, I. Sinning, and S. Cusack, Science 294 (5542), 598 (2001).ADSCrossRefGoogle Scholar
  29. 29.
    G. L. Conn, Science 284 (5417), 1171 (1999).ADSCrossRefGoogle Scholar
  30. 30.
    D. Moras and A. Poterszman, Curr. Biol. 6 (5), 530 (1996).CrossRefGoogle Scholar
  31. 31.
    A. Barik and R. P. Bahadur, Nucleic Acids Res. 42 (15), 10148 (2014).CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2017

Authors and Affiliations

  1. 1.Department of PhysicsMoscow State UniversityMoscowRussia
  2. 2.National Research University Higher School of EconomicsMoscowRussia

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