Strategies for RNA-Guided DNA Recombination

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


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.


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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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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