Why yeast?

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Model organism genetics and human disease
With an emphasis on.. APOYG!

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Model Organisms
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Not so many genes!
19,000
14,000
21,000
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Why we love yeast
Model organism Eukaryotic intracellular
biology Gene function conservation (e.g.,
human disease genes) Testbed for genomic
technologies

Experimental approaches Classical genetics
(biochemistry) Recombinant genetics Emerging
technologies
Community of yeast people Open exchange of
ideas, reagents, results Collaboration
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Saccharomyces cerevisiae Budding yeastThe
E.coli of eukaryotic cells
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Yeast vs. Human
50 of yeast genes have at least one similar
human gene
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Human disease genes in model organisms
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Human disease genes in model organisms
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APOYG and Disease Two examples Zelwegers
Syndrome Peroxisome biogenesis Colorectal
Cancer Genome instability

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Zellweger Spectrum
Zellweger syndrome
Neonatal adreno- leukodystrophy
Infantile Refsum Disease
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Zellweger Patient Cells Share a Common Phenotype
with Yeast pex Mutants
Zellweger patient
Control
Human
???? PTS1)
Wild-type
pex mutant
Yeast
(PTS1 - GFP)
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Strategies for Mammalian PEX Gene Identification

• Functional complementation Mammalian cDNA
  expression libraries
• Homology probing
• Identify all yeast peroxins
• Identify all homologous human proteins
• Test as candidate genes

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Yeast / Human Connections
Human
Identification
Function
Yeast
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Discovery of Yeast and Human PEX Genes
Yeast
PEX Genes
Human
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Cancer
C. Rieder
If you want to understand cancer, you need
answers to the many questions about the role
genome instability plays. ---Bert Vogelstein,
2002
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Genetic Instability in Human Cancers
MIN Microsatellite instability
(increased mutation rate)

CIN Chromosome instability
(increased aneuploidy rate)
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Metaphase
Anaphase
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Spindle Checkpoint
Improperly attached kinetochore
Bub1, Bub3,
Mad1, Mad2, Mad3
Cohesin
APCCdc20
Separase
Securin
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hBUB1
Spindle Checkpoint
Improperly attached kinetochore
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Bub1, Bub3,
Mad1, Mad2, Mad3
hMRE11
Cohesin
APCCdc20
Separase
Securin
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hDING
hCDC4
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Yeast as a model CIN biology (gene
function) CIN candidate genes- (Cancer CIN
genes) Therapeutics Finding an Achilles
heel of cancer
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What are all the proteins mutable to CIN?

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Colony Sectoring Assay
Chromosome Transmission Fidelity (ctf) Screen
non-essential Chromosome Fragment
SUP11
M

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Summary of the 26 Cloned ctf Mutants
ctf alleles Gene Name Essential? Function
1 30 CTF1/CHL1 Cohesion (helicase)
2 11 TOF1/CTF2 Cohesion, replication
3 11 CTF3 Kinetochore protein
4 8 CTF4/CHL15/POB1 Cohesion (establishment)
5 5 CTF5/MCM21 Kinetochore protein
6 5 CTF6/RAD61 Cohesion
7 5 CTF7/ECO1 Yes Cohesion (establishment)
8 9 3 3 CTF8 SMC3/CTF9 Cohesion (alternative RFC) Cohesion (cohesin subunit)
10 3 CDC6/CTF10 Yes DNA replication
11 3 PDS5/CTF11 Yes Cohesion (cohesin associated)
12 3 CTF12/SCC2 Yes Cohesion (cohesin loading)
18 3 CTF18/CHL12 Cohesion (alternative RFC)
13 1 CTF13 Yes Kinetochore protein (CBF3)
14 1 CTF14/NDC10 Yes Kinetochore protein (CBF3)
15 1 CTF15/RPB4 Subunit of RNA polymerase II
17 2 CTF17/MCM17/CHL4 Kinetochore protein
19 2 CTF19 Kinetochore protein
s3 1 BIM1 Microtubule binding
s127 1 SIC1 Cdk inhibitor
s138 1 SPT4 Chromatin structure
s141 1 NUP170 Nucleoporin
s143 1 MAD1 Spindle checkpoint
s155 1 MCM16 Kinetochore protein
s165 1 SCC3 Yes Cohesion (cohesin subunit)
s166 1 SMC1 Yes Cohesion (cohesin subunit)
Kinetochore proteins Cohesion DNA /RNA metabolism
Yes
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S. cerevisiae Genome Deletion Project

• Complete set of yeast nonessential deletion
  mutants
• 4,700 haploid strains
• 4,700 homozygous diploid strains
• nonessential genes deleted with kanMX
  fifty 96 well plate
• 5,800 heterozygous diploid strains

condense 4 plates onto 1
pin 96 strains onto G418 plates
96 well plate frozen glycerol stock
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The yeast gene knockout collection
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Yeast CIN genes300 non-essential genes (85
coverage)100 essential genes (and still
counting)
Human homologs?
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12 yeast CIN genes have top-hit human homologs
that are mutated in cancers
Gene Top Human Hit E-value Cancer Type/Cancer syndromes
ADE17 ATIC 0 anaplastic large cell lymphoma
RAD54 RAD54L 1E-164 Lymphoma,n-Hodgkin Breastcancer, invasiveintraductal Colon adecarcima
TPD3 PPP2AR 1E-133 Lungcancer
RAD51 RAD51 1E-122 Susceptibility to breast cancer
RDH54 RAD54B 1E-121 Lymphoma,n-Hodgkin Colonadecarcima
SGS1 BLM 1E-115 Bloomsyndrome leukemia, lymphoma, skin squamous cell, other cancers
RAD1 ERCC4 1E-109 Xeroderma pigmentosum, groupF skin basal cell, skin squamous cell, melama
MRE11 MRE11A 1E-108 Ataxia-telangiectasia-like disorder, colorectal cancer with CIN
DUN1 CHK2 6E-55 Li-Fraumeni syndrome Osteosarcoma, somatic Prostatecancer, familial Susceptibility to breast and colorectal cancer
BUB1 BUB1 1E-41 Colorectal cancer with CIN
MAD1 MAD1L 5E-12 Lymphoma, somatic Prostatecancer, somatic
CDC73 parafibromin 9E-12 Hyperparathyroidism-jaw tumor syndrome Hyperparathyroidism, familial primary Parathyroid adema with cystic changes
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CIN mutational spectrum in cancer- Why? Cancer
biology Tumor classification Identification of
new drug targets CIN gene / Synthetic Lethal
gene pairs


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Synthetic Lethality
yfg2
Viable
Viable
yfg1
Dead
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Yeast Genetic Interactions
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12 yeast CIN genes have human homologs that are
mutated in cancers
Gene Top Human Hit E-value Cancer Type/Cancer syndromes
ADE17 ATIC 0 anaplastic large cell lymphoma
RAD54 RAD54L 1E-164 Lymphoma,n-Hodgkin Breastcancer, invasiveintraductal Colon adecarcima
TPD3 PPP2AR 1E-133 Lungcancer
RAD51 RAD51 1E-122 Susceptibility to breast cancer
RDH54 RAD54B 1E-121 Lymphoma,n-Hodgkin Colonadecarcima
SGS1 BLM 1E-115 Bloomsyndrome leukemia, lymphoma, skin squamous cell, other cancers
RAD1 ERCC4 1E-109 Xeroderma pigmentosum, groupF skin basal cell, skin squamous cell, melama
MRE11 MRE11A 1E-108 Ataxia-telangiectasia-like disorder, colorectal cancer with CIN
DUN1 CHK2 6E-55 Li-Fraumeni syndrome Osteosarcoma, somatic Prostatecancer, familial Susceptibility to breast and colorectal cancer
BUB1 BUB1 1E-41 Colorectal cancer with CIN
MAD1 MAD1L 5E-12 Lymphoma, somatic Prostatecancer, somatic
CDC73 parafibromin 9E-12 Hyperparathyroidism-jaw tumor syndrome Hyperparathyroidism, familial primary Parathyroid adema with cystic changes
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Yeast CIN Genes and Human Cancer
CIN candidate genes Somatic mutations in
colon cancer 40 spectrum in 11 genes Cancer
therapeutics Achilles heel candidate
genes Validation in mammalian cells

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Four volumes of the Encyclopedia of Life
21,000
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Human genome sequence completed
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10,000 parts
4,000,000 parts
20,000 genes
6,000 genes
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Power of Model Organism Research Genetics,
biochemistry, genomics Basic biology Human
health Human disease Therapy Preventative
medicine

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