Download Lab meeting, November 8, 2004

Gene Order Evolution:
The consequences of genome rearrangements
1
Why do we care?
• Impact of genome rearrangements
• Diseases
• Organismal evolution
2
Genome rearrangement
“Transfer of a segment of DNA to a new position on the
same or another chromosome”
3
Method
• Our approach: systematic,whole-genome
• Microarray based analysis
• High level of resolution
• Strains of S. cerevisiae
• S90 – sequence strain like
• Y101 – known deletions
4
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:
5
1 dup: 1 del:
2 single copy
6
Are there differences between two similar
strains?
Where are the differences located?
Do these changes effect gene
expression?
7
Are there differences between two similar
strains?
Where are the differences located?
Do these changes effect gene
expression?
8
Comparative Genomic Hybridization
• 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
9
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
10
Possibly Transposed Spots
11
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 56.7
Hotspots*
42.7
2.15
Transposable 29.5
Elements
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)
12
Distribution of Possibly
Transposed Spots
Transposable Elements
0.9
0.8
0.7
R2 = 0.976
Fraction of spots
0.6
0.5
Our spots
Random spots
Linear (Random spots)
0.4
0.3
0.2
0.1
0
0
5
10
15
20
25
30
35
40
45
Window (kb)
13
Are there differences between two similar
strains?
Where are the differences located?
Do these changes effect gene
expression?
14
Genome Mismatch Scanning
Digested DNA
Spore DNA
Parental DNA
Mix, denature, reanneal
Select heterohybrids based on hemi-methylation
Remove mismatches via MutHLS cleavage
Hybridize remaining DNA
-result = 0 or 1
15
GMS analysis
Tetrad 27c- Chromosome 15
8
6
4
2
Score
Smooth
Raw
0
0
200000
400000
600000
800000
1000000
1200000
-2
-4
-6
-8
Position
16
Predicting CGH using GMS
Y101
S90
C1
C1
C2
C2
17
Predicting CGH using GMS
Y101
S90
C1
C1
C2
C2
18
Are there differences between two similar
strains?
Where are the differences located?
Do these changes effect gene
expression?
19
Expression data (future)
• Coexpression of transposed vs nontransposed genes
• Neighbor effect on expression
20
GMS Data Set
21