Models of recombination in ciliates

Ciliate is a term applied to any member of a group of around 10,000 different types of single-celled organisms that are characterised by two unique features: the possession of hair-like cilia for movement, and the presence of two nuclei instead of the usual one. One nucleus (the micronucleus) is used for sexual exchange of DNA, and the other (the macronucleus) is responsible for cell growth and proliferation. Crucially, the micronucleus contains an “encoded” description of the working macronucleus, which is decoded during development. This encoding “scrambles” functional gene elements by both the permutation of coding sequences and the inclusion of non-coding sequences. A picture of the ciliate Oxytricha nova is shown in Fig. 1. During development, ciliates reorganise the material in the micronucleus by removing non-coding sequences and placing coding sequences in the correct order. This ‘unscrambling’ may be interpreted as a computational process during which up to 95% of the original sequence is discarded. The exact mechanism by which genes are unscrambled is not yet fully understood. We first describe experimental observations that have at least suggested possible mechanisms. We then describe two different models of the process. We conclude with a discussion of the computational and biological implications of this work.