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Strategies for RNA-Guided DNA Recombination

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Algorithmic Bioprocesses

Part of the book series: Natural Computing Series ((NCS))

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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.

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Author information

Authors and Affiliations

  1. University of South Florida, Tampa, FL, USA

    Angela Angeleska, Nataša Jonoska & Masahico Saito

  2. Princeton University, Princeton, NJ, USA

    Laura F. Landweber

Authors
  1. Angela Angeleska
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  2. Nataša Jonoska
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  3. Masahico Saito
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  4. Laura F. Landweber
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Corresponding author

Correspondence to Angela Angeleska .

Editor information

Editors and Affiliations

  1. Dept. Computer Science, University of British Columbia, Main Mall 201-2366, Vancouver, V6T 1Z4, Canada

    Anne Condon

  2. Dept. Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel

    David Harel

  3. Leiden Inst. Advanced Computer Science, Leiden University, Niels Bohrweg 1, Leiden, 2333 CA, Netherlands

    Joost N. Kok

  4. Turku Centre for Computer Science, Lemminkaisenkatu 14 A, Turku, 20520, Finland

    Arto Salomaa

  5. Computer Science, Computation,, California Inst. of Technology, Pasadena, 91125, U.S.A.

    Erik Winfree

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© 2009 Springer-Verlag Berlin Heidelberg

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Angeleska, A., Jonoska, N., Saito, M., Landweber, L.F. (2009). Strategies for RNA-Guided DNA Recombination. In: Condon, A., Harel, D., Kok, J., Salomaa, A., Winfree, E. (eds) Algorithmic Bioprocesses. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88869-7_6

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  • DOI: https://doi.org/10.1007/978-3-540-88869-7_6

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  • Print ISBN: 978-3-540-88868-0

  • Online ISBN: 978-3-540-88869-7

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