We have developed a fluorescent in situ hybridization (FISH) method to examine 
the structure of both natural chromosomes and small artificial chromosomes 
during the mitotic cycle of budding yeast. Our results suggest that the pairing 
of sister chromatids: (a) occurs near the centromere and at multiple places 
along the chromosome arm as has been observed in other eukaryotic cells; (b) is 
maintained in the absence of catenation between sister DNA molecules; and (c) is 
independent of large blocks of repetitive DNA commonly associated with 
heterochromatin. Condensation of a unique region of chromosome XVI and the 
highly repetitive ribosomal DNA (rDNA) cluster from chromosome XII were also 
examined in budding yeast. Interphase chromosomes were condensed 80-fold 
relative to B form DNA, similar to what has been observed in other eukaryotes, 
suggesting that the structure of interphase chromosomes may be conserved among 
eukaryotes. While additional condensation of budding yeast chromosomes were 
observed during mitosis, the level of condensation was less than that observed 
for human mitotic chromosomes. At most stages of the cell cycle, both unique and 
repetitive sequences were either condensed or decondensed. However, in cells 
arrested in late mitosis (M) by a cdc15 mutation, the unique DNA appeared 
decondensed while the repetitive rDNA region appeared condensed, suggesting that 
the condensation state of separate regions of the genome may be regulated 
differently. The ability to monitor the pairing and condensation of sister 
chromatids in budding yeast should facilitate the molecular analysis of these 
processes as well as provide two new landmarks for evaluating the function of 
important cell cycle regulators like p34 kinases and cyclins. Finally our FISH 
method provides a new tool to analyze centromeres, telomeres, and gene 
expression in budding yeast.