Collisions between yeast chromosomal loci in vivo are governed by three layers of organization

The relative probabilities that different pairs of chromosomal loci will co llide with one another in vegetatively growing diploid yeast cells have bee n assessed using a genetic assay for Cre/loxP site-specific recombination. Recombination rates have been determined for 18 different pairs of loxP sit es representing diverse pairs of positions within the genome. Overall, rela tive collision probabilities vary over an eightfold range. Within this rang e, a hierarchy comprising three levels of organization can be discerned. Fi rst, collisions between loci on nonhomologous chromosomes are governed by n onspecific centromere clustering. Second, a sequence is closer to allelic o r nearby sequences on its homolog than to sequences on nonhomologous chromo somes, an effect most simply attributed to homolog pairing. Third, a sequen ce can be closer to other sequences nearby on the same chromosome than to s equences on other chromosomes. These findings provide a framework for asses sing the role of chromosome disposition in cellular processes such as DNA r epair and gene expression. Also the possibility is raised that genome-wide coalignment of homologs is not the fundamental raison d'etre of the somatic pairing process. We suggest instead that pairing may exist to promote juxt aposition of homologous regions within irregular genome complements.