On the role of homologous sequences in chromosomal rearrangements

Deletions and other chromosomal rearrangements can be generated by recombination between repeated sequences. It has been shown in a number of systems that the probability of exchange or gene conversion decreases with increasing distance between repeats. This paper examines the question of how repeats find each other, using deletion formation in bacteriophage T4 as a model system. Homologous sequences adjacent to the repeats can either stimulate or inhibit recombination, depending on their orientation. I present evidence that the spatial separation between repeats is the key determinant of the distance dependence and conclude that adjacent homologous sequences affect recombination by aligning chromosomes so as to position the recombining sites either closer together or farther apart. Analogous examples of apparent 'targeting' by homologous sequences in eukaryotes and other prokaryotes are noted.