An Exactly Solvable Model of Random Site-Specific Recombinations

Wei, Y., Koulakov, A. A. (December 2012) An Exactly Solvable Model of Random Site-Specific Recombinations. Bulletin of Mathematical Biology, 74 (12). pp. 2897-20. ISSN 00928240

URL: http://www.ncbi.nlm.nih.gov/pubmed/23151958
DOI: 10.1007/s11538-012-9788-z

Abstract

Cre-lox and other systems are used as genetic tools to control site-specific recombination (SSR) events in genomic DNA. If multiple recombination sites are organized in a compact cluster within the same genome, a series of random recombination events may generate substantial cell specific genomic diversity. This diversity is used, for example, to distinguish neurons in the brain of the same multicellular mosaic organism, within the brainbow approach to neuronal connectome. In this paper, we study an exactly solvable statistical model for SSR operating on a cluster of recombination sites. We consider two types of recombination events: inversions and excisions. Both of these events are available in the Cre-lox system. We derive three properties of the sequences generated by multiple recombination events. First, we describe the set of sequences that can in principle be generated by multiple inversions operating on the given initial sequence. We call this description the ergodicity theorem. On the basis of this description, we calculate the number of sequences that can be generated from an initial sequence. This number of sequences is experimentally testable. Second, we demonstrate that after a large number of random inversions every sequence that can be generated is generated with equal probability. Lastly, we derive the equations for the probability to find a sequence as a function of time in the limit when excisions are much less frequent than inversions, such as in shufflon sequences.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > recombination
CSHL Authors:
Communities: CSHL labs > Koulakov lab
CSHL Post Doctoral Fellows
Depositing User: Matt Covey
Date: December 2012
Date Deposited: 17 Jan 2013 19:39
Last Modified: 03 May 2013 15:34
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27078

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