Abstract #16

Experimental Evolution Of High-Copy Ty1 Strains. Lisa Z. Scheifele^1,2, Maitreya J. Dunham³, Sarah J. Wheelan^1,2, Jef D. Boeke^1,2. 1) Molecular Biology and Genetics; 2) The High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD; 3) Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ.
   Ty elements have been implicated as mediators of chromosomal rearrangements during experimental evolution (Adams PNAS 1986, Dunham PNAS 2002). To determine if Ty elements are causative in the formation of genomic rearrangements, we derived independent cell lines termed ultra-high copy (UHC) strains that vary in Ty copy number up to 13-fold higher than the parental strain. The genomic location of these introduced Ty1 elements has been mapped with custom tiling microarrays (Transposon Insertion site Profiling-chips). High transposon copy number increases the potential for ectopic recombination, and indeed, UHC strains are sensitive to DNA damaging agents. Yet, because that instability could enable genome evolution, we examined chromosomal alterations following chemostat evolution of UHC strains.
   We presumed that UHC strains would accumulate mutations at a higher rate, but find minimal difference in the frequency of periodic shifts between wild-type and high-copy strains. While the frequency of adaptive shifts may not be altered in UHC strains, the spectrum of rearrangements may be broader; indeed, we find remarkable variation both in growth and in sensitivity to hydroxyurea (HU) in evolved strains, suggesting they differ in DNA repair proficiency. As well, pulsed-field gel electrophoresis of evolved clones indicates greater heterogeneity in karyotypic changes of high-copy strains. Using array comparative genomic hybridization (aCGH) to map the chromosomal breakpoints, we discovered that before the evolution one high-copy Ty1 strain spontaneously became diploid, carrying a deletion on one chromosome of the region between MATa and HMRa. Although the predominant translocation in the evolved UHC population is identical to wild-type, further studies will determine if the variability seen in evolved clones in growth rate, HU sensitivity and electrophoretic karyotype will be visible by aCGH.

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