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Gene Order Evolution:The consequences of genome rearrangements

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Why do we care?

• Impact of genome rearrangements• Diseases

• Organismal evolution

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

Genome rearrangement

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Method

• Our approach: systematic,whole-genome • Microarray based analysis

• High level of resolution

• Strains of S. cerevisiae• S90 – sequence strain like

• Y101 – known deletions

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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:

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1 dup: 1 del: 2 single copy

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• Are there differences between two similar strains?

• Where are the differences located?

• Do these changes effect gene expression?

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Are there differences between two similar strains?

Where are the differences located?

Do these changes effect gene expression?

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• 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

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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

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Possibly Transposed Spots

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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)

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Distribution of Possibly Transposed Spots

Transposable Elements

R2 = 0.976

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0.1

0.2

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0.4

0.5

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0.7

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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)

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Are there differences between two similar strains?

Where are the differences located?

Do these changes effect gene expression?

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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

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GMS analysisTetrad 27c- Chromosome 15

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-6

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-2

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0 200000 400000 600000 800000 1000000 1200000

Position

Sco

re

Smooth

Raw

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Predicting CGH using GMS

Y101 S90C1 C1

C2 C2

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Predicting CGH using GMS

Y101 S90C1 C1

C2 C2

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Are there differences between two similar strains?

Where are the differences located?

Do these changes effect gene expression?

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Expression data (future)

• Coexpression of transposed vs non-transposed genes

• Neighbor effect on expression

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GMS Data Set

Absolute Value of Raw GMS Score Frequency

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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