Strategies of Loop Recombination in Ciliates

TL;DR

This paper analyzes the possible loop recombination operations in ciliates during gene assembly, providing a characterization of their applicability and order in transforming micronuclear to macronuclear DNA.

Contribution

It introduces a formal framework for understanding which loop recombination operations can be applied and in what sequence during gene assembly in ciliates.

Findings

Characterization of applicable loop recombination operations

Determination of the order of operations for gene transformation

Framework applicable to legal strings in gene assembly

Abstract

Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronucleus. In this paper we characterize which loop recombination operations (one of the three types of molecular operations that accomplish gene assembly) can possibly be applied in the transformation of a given gene from its micronuclear form to its macronuclear form. We also characterize in which order these loop recombination operations are applicable. This is done in the abstract and more general setting of so-called legal strings.