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Strategies for RNA-Guided DNA Recombination

  • Angela AngeleskaEmail author
  • Nataša Jonoska
  • Masahico Saito
  • Laura F. Landweber
Chapter
Part of the Natural Computing Series book series (NCS)

Abstract

We present a model for homologous DNA recombination events guided by double-stranded RNA (dsRNA) templates, and apply this model to DNA rearrangements in some groups of ciliates, such as Stylonychia or Oxytricha. In these organisms, differentiation of a somatic macronucleus from a germline micronucleus involves extensive gene rearrangement, which can be modeled as topological braiding of the DNA, with the template-guided alignment proceeding through DNA branch migration. We show that a graph structure, which we refer to as an assembly graph, containing only 1- and 4-valent vertices can provide a physical representation of the DNA at the time of recombination. With this representation, 4-valent vertices correspond to the alignment of the recombination sites, and we model the actual recombination event as smoothing of these vertices.

Keywords

Open Path Pointer Sequence Polygonal Path Assembly Graph Branch Migration 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Angeleska A, Jonoska N Saito M (2009) Discrete Appl Math (accepted) Google Scholar
  2. 2.
    Angeleska A, Jonoska N, Saito M, Landweber LF (2007) J Theor Biol 248(4):706–720 CrossRefGoogle Scholar
  3. 3.
    Brijder R, Hoogeboom HJ, Rozenberg G (2007) From micro to macro: how the overlap graph determines the reduction graph in ciliates. In: Lecture notes in computer science, vol 4639. Springer, Berlin, pp 149–160 Google Scholar
  4. 4.
    Cavalcanti ARO, Landweber LF (2006) Insights into a biological computer: detangling scrambled genes in ciliates. In: Chen J, Jonoska N, Rozenberg G (eds) Nanotechnology: science and computation. Springer, Berlin Google Scholar
  5. 5.
    Chang WJ, Kuo S, Landweber LF (2006) Gene 368:72–77 CrossRefGoogle Scholar
  6. 6.
    Ehrenfeucht A, Harju T, Petre I, Prescott DM, Rozenberg G (2005) Computing in living cells. Springer, Berlin Google Scholar
  7. 7.
    Ehrenfeucht A, Harju T, Rozenberg G (2002) Theor Comput Sci 281:325–349 zbMATHCrossRefMathSciNetGoogle Scholar
  8. 8.
    Garnier O, Serrano V, Duharcourt S, Meyer E (2004) Mol Cell Biol 24:7370–7379 CrossRefGoogle Scholar
  9. 9.
    Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006) Nature 442:199–202 Google Scholar
  10. 10.
    Head T (1987) Bull Math Biol 49:737–759 zbMATHMathSciNetGoogle Scholar
  11. 11.
    Jonoska N, Saito M (2004) Algebraic and topological models for DNA recombinant processes. In: Calude CS, Calude E, Dinneen MJ (eds) Developments in language theory. Lecture notes in computer science, vol 3340. Springer, Berlin, pp 49–62 Google Scholar
  12. 12.
    Juranek SA, Rupprecht S, Postberg J, Lipps HJ (2005) Eukaryot Cell 4:1934–1941 CrossRefGoogle Scholar
  13. 13.
    Kari L, Landweber LF (1999) Computational power of gene rearrangement. In: Winfree E, Gifford DK (eds) DNA based computers. AMS, Reading, pp 207–216 Google Scholar
  14. 14.
    Kauffman LH (1991) Knots and physics. Series on knots and everything, vol 1. World Scientific, Singapore zbMATHGoogle Scholar
  15. 15.
    Landweber LF (2007) Science 318:405–406 CrossRefGoogle Scholar
  16. 16.
    Kuo S, Chang W-J, Landweber LF (2006) Mol Biol Evol 23(1):4–6 CrossRefGoogle Scholar
  17. 17.
    Mochizuki K, Fine NA, Fujisawa T, Gorovsky MA (2002) Cell 110:689–699 CrossRefGoogle Scholar
  18. 18.
    Mollenbeck M, Zhou Y, Cavalcanti ARO, Jonsson F, Higgins BP, Chang WJ, Juranek S, Doak TG, Rozenberg G, Lipps HJ, Landweber LF (2008) PLoS ONE 3(6):e2330. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002330 CrossRefGoogle Scholar
  19. 19.
    Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, Landweber LF (2008) Nature 451:153–158 CrossRefGoogle Scholar
  20. 20.
    Prescott DM, Greslin AF (1992) Dev Genet 13(1):66–74 CrossRefGoogle Scholar
  21. 21.
    Prescott DM, Ehrenfeucht A, Rozenberg G (2003) J Theor Biol 222:323–330 CrossRefMathSciNetGoogle Scholar
  22. 22.
    Seeman NC (2003) Nature 421:427–431 CrossRefMathSciNetGoogle Scholar
  23. 23.
    Sumners DW (1995) Lifting the curtain: using topology to probe the hidden action of enzymes. Not 42(5):528–537 zbMATHMathSciNetGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Angela Angeleska
    • 1
    Email author
  • Nataša Jonoska
    • 1
  • Masahico Saito
    • 1
  • Laura F. Landweber
    • 2
  1. 1.University of South FloridaTampaUSA
  2. 2.Princeton UniversityPrincetonUSA

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