Processes of copy number change in human DNA : The dynamics of α-globin gene deletion

Kwan-Wood G Lam, Alec J Jeffreys
Department of Genetics, University of Leicester, Adrian Building, University Road, LE1 7RH, United Kingdom

Ectopic recombination between locally repeated DNA sequences is of fundamental importance in the evolution of gene families, generating copy number variation in human DNA and often leading to pathological rearrangements. Despite its importance, little is known about the dynamics and processes of these unequal crossovers and the degree to which meiotic recombination plays a role in instability. We address this issue using as a highly informative system the duplicated α-globin genes in which ectopic recombination can lead to gene deletions, often very prevalent in populations affected by malaria, as well as reduplications. We show that spontaneous deletions can be accessed directly in genomic DNA using single DNA molecule methods. These deletions proved to be remarkably common in both blood and sperm. Somatic deletions arise by a strictly intra-chromosomal pathway of homologous exchange that also operates in the germline and can generate mutational mosaicism, while sperm deletions frequently involve recombinational interactions between homologous chromosomes that most likely occur at meiosis. Almost all deletions arise by simple exchange between homologous DNA sequences, though some show evidence of patchy gene conversion near the site of ectopic exchange. Ectopic recombination frequencies show surprisingly little requirement for long, identical homology blocks shared by paralogous sequences, and exchanges can occur even between short regions of sequence identity.