1. 1 Gene Order Evolution: The consequences of genome rearrangements

2. 2 Why do we care? Impact of genome rearrangements Diseases Organismal evolution

3. 3 “Transfer of a segment of DNA to a new position on the same or another chromosome” Genome rearrangement

4. 4 Method Our approach: systematic,whole-genome Microarray based analysis High level of resolution Strains of S. cerevisiae S90 – sequence strain like Y101 – known deletions

5. 5 Yeast Refresher Small, well-studied genome 12 Mbp, 16 chromosomes, 5.7k genes Produces 4 spores on tetrads – these are meitotic products Important for our analysis is the fact that, if two strains differ in gene order, 2/3 of the tetrads that result from a cross between them will have the following pattern:

6. 6 1 dup: 1 del: 2 single copy

7. 7 Are there differences between two similar strains? Where are the differences located? Do these changes effect gene expression?

8. 8 Are there differences between two similar strains? Where are the differences located? Do these changes effect gene expression?

9. 9 Compare CGH results of parents and spores to reference Normal (1 copy) 1:1 Ratio of Cy3 and Cy5 Duplication (2 copies) Low ratio of Cy3:Cy5 Deleted (0 copies) High ratio of Cy3:Cy5 Comparative Genomic Hybridization

10. 10 Computational Analysis SpotProb- written by Dr. Todd Vision to find spots that show a 1 deletion: 1 duplication: 2 single copy pattern Added constraint that both parents must have a single copy

11. 11 Possibly Transposed Spots

12. 12 Distribution of Possibly Transposed Spots Possible Areas Of Recombination Avg. Dist. (kB) Expected Avg. Dist. (kB) Z-Score tRNA genes30.926.91.0 Recombination Hotspots* 56.742.72.15 Transposable Elements 29.533.8-0.9 --Delta32.139.6-1.5 --OmegaN/A --Sigma216237-0.5 --Tau3753181.3 *Gerton et al.(2000)

13. 13 Distribution of Possibly Transposed Spots

14. 14 Are there differences between two similar strains? Where are the differences located? Do these changes effect gene expression?

15. 15 Genome Mismatch Scanning Spore DNA Parental DNA Mix, denature, reanneal Digested DNA Select heterohybrids based on hemi-methylation Remove mismatches via MutHLS cleavage Hybridize remaining DNA -result = 0 or 1

16. 16 GMS analysis

17. 17 Predicting CGH using GMS Y101 S90 C1 C2

18. 18 Predicting CGH using GMS Y101 S90 C1 C2

19. 19 Are there differences between two similar strains? Where are the differences located? Do these changes effect gene expression?

20. 20 Expression data (future) Coexpression of transposed vs non- transposed genes Neighbor effect on expression

21. 21 GMS Data Set