Determination of intrachromosomal recombination rates in cultured mammalian cells

Recombination is involved in many important biological processes including DNA repair, gene expression, and generation of genetic diversity. Recombination must be carefully regulated so as to prevent the deleterious consequences that may result from rearrangements between dissimilar sequences in a genome. It is of considerable interest to study the mechanisms by which genetic rearrangements in mammalian chromosomes are regulated in order to understand better how genomic integrity is normally maintained and to gain insight into the types of genetic mutations that may destabilize the genome. To explore such issues in mammalian chromosomes, a suitable experimental system must be developed. In this chapter, we describe a model system for studying intrachromosomal recombination in cultured mammalian cells. We discuss two model recombination substrates, a method for stably introducing the substrates into cultured Chinese hamster ovary cells, and a method for determining rates of intrachromosomal recombination between sequences contained within the integrated substrates. The general approach described here should be applicable to the study of a variety of aspects of recombination in virtually any cultured mammalian cell line.