Computational nature of gene assembly in ciliates

Abstract

Ciliates are a very diverse and ancient group of unicellular eukaryotic organisms. A feature that is essentially unique to ciliates is the nuclear dualism, meaning that they have two functionally different types of nuclei, the macronucleus and the micronucleus. During sexual reproduction a micronucleus is transformed into a macronucleus-this process is called gene assembly, and it is the most involved naturally occurring example of DNA processing that is known to us. Gene assembly is a fascinating research topic from both the biological and the computational points of view. In this chapter, several approaches to the computational study of gene assembly are considered. This chapter is self-contained in the sense that the basic biology of gene assembly as well as mathematical preliminaries are introduced. Two of the most studied molecular models for gene assembly, intermolecular and intramolecular, are presented and the main mathematical approaches used in studying these models are discussed. The topics discussed in more detail include the string and graph rewriting models, invariant properties, templatebased DNA recombination, and topology-based models. This chapter concludes with a brief discussion of a number of research topics that, because of the space restrictions, could not be covered in this chapter.