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Vol. 13, No. 14, pp. 1871-1883, July 15, 1999
Department of Molecular and Cellular Biology, Harvard University,
Cambridge, Massachusetts 02138 USA
The relative probabilities that different pairs of chromosomal loci
will collide with one another in vegetatively growing diploid yeast
cells have been assessed using a genetic assay for Cre/loxP site-specific recombination.
Recombination rates have been determined for 18 different pairs of
loxP sites representing diverse pairs of positions within the
genome. Overall, relative collision probabilities vary over an
eightfold range. Within this range, a hierarchy comprising three levels
of organization can be discerned. First, collisions between loci on
nonhomologous chromosomes are governed by nonspecific centromere
clustering. Second, a sequence is closer to allelic or nearby sequences
on its homolog than to sequences on nonhomologous chromosomes, an effect most simply attributed to homolog pairing. Third, a sequence can
be closer to other sequences nearby on the same chromosome than to
sequences on other chromosomes. These findings provide a framework for
assessing the role of chromosome disposition in cellular processes such
as DNA repair 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 juxtaposition of homologous regions within
irregular genome complements.
[Key Words: Saccharomyces cerevisiae; site-specific recombination; chromosome; nucleus; homolog pairing; DNA repair]
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