An exactly solvable model of random site-specific recombinations

DOI10.1007/S11538-012-9788-ZzbMATH Open1264.92021arXiv1112.5678OpenAlexW3104665395WikidataQ42292967 ScholiaQ42292967MaRDI QIDQ1936690FDOQ1936690

Authors: Yi Wei, Alexei A. Koulakov 

Publication date: 6 February 2013

Published in: Bulletin of Mathematical Biology (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/1112.5678

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zbMATH Keywords

ergodicityMarkov processesSSR

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10)

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