1 Gene Order Evolution: The consequences of genome rearrangements
1
Gene Order Evolution:The consequences of genome rearrangements
2
Why do we care?
• Impact of genome rearrangements• Diseases
• Organismal evolution
3
“Transfer of a segment of DNA to a new position on the same or another chromosome”
Genome rearrangement
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
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
1 dup: 1 del: 2 single copy
7
• Are there differences between two similar strains?
• Where are the differences located?
• Do these changes effect gene expression?
8
Are there differences between two similar strains?
Where are the differences located?
Do these changes effect gene expression?
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
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
Possibly Transposed Spots
12
Distribution of Possibly Transposed Spots
Possible Areas Of Recombination
Avg. Dist. (kB)
Expected Avg. Dist. (kB)
Z-Score
tRNA genes 30.9 26.9 1.0
Recombination Hotspots*
56.7 42.7 2.15
Transposable Elements
29.5 33.8 -0.9
--Delta 32.1 39.6 -1.5
--Omega N/A N/A N/A
--Sigma 216 237 -0.5
--Tau 375 318 1.3
*Gerton et al.(2000)
13
Distribution of Possibly Transposed Spots
Transposable Elements
R2 = 0.976
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
0 5 10 15 20 25 30 35 40 45
Window (kb)
Fra
ctio
n o
f sp
ots
Our spots
Random spots
Linear (Random spots)
14
Are there differences between two similar strains?
Where are the differences located?
Do these changes effect gene expression?
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
GMS analysisTetrad 27c- Chromosome 15
-8
-6
-4
-2
0
2
4
6
8
0 200000 400000 600000 800000 1000000 1200000
Position
Sco
re
Smooth
Raw
17
Predicting CGH using GMS
Y101 S90C1 C1
C2 C2
18
Predicting CGH using GMS
Y101 S90C1 C1
C2 C2
19
Are there differences between two similar strains?
Where are the differences located?
Do these changes effect gene expression?
20
Expression data (future)
• Coexpression of transposed vs non-transposed genes
• Neighbor effect on expression
21
GMS Data Set
Absolute Value of Raw GMS Score Frequency
0
0.05
0.1
0.15
0.2
0.25
0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.2 3.4 3.6 3.8 4 More
Score
FlaggedSpotsAll Spots