What can we learn from microarrays about gene expression patterns

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What can we learnfrom microarrays about gene
expression patterns?
presentated by Sonja Prohaska
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the Biochemistry Departement of Stanford.They
usedDNA Microarray toanalyze changes in the
genomic expression patternsin response to divers
enviromentals stresses
A question also asked by...
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Measuring transcription levels over time,they
tried to gain information about...

• temporal gene expression patterns after exposure
  to stress
• dose response to stress
• steady-state gene expression patterns after
  adaptation to stress

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Therefore they had to...

• expose yeast to divers enviromental conditions
• prepare probe and hybridisize to microarray
• compare data
• do hierarchical clustering
• search for sequence motive

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Therefore they had to...

• expose yeast to divers enviromental conditions
• prepare probe and hybridisize to microarray
• compare data
• do hierarchical clustering
• search for sequence motive

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expose yeast to divers enviromental conditions

• sudden heat shock (25c to 37)
• hydrogen peroxid (H2O2)
• menadion bisulfite
• dithiothrietol (DTT)
• diamide -gt sulfhydryl-oxidizing agent
• hyperosmotic shock (sorbitol)
• starvetion

7
Therefore they had to...

• expose yeast to divers enviromental conditions
• prepare probe and hybridisize to microarray
• compare data
• do hierarchical clustering
• search for sequence motive

8
Therefore they had to...

• expose yeast to divers enviromental conditions
• prepare probe and hybridisize to microarray
• compare data
• do hierarchical clustering
• search for sequence motive

9
Therefore they had to...

• expose yeast to divers enviromental conditions
• prepare probe and hybridisize to microarray
• compare data
• do hierarchical clustering
• search for sequence motive

10
Therefore they had to...

• expose yeast to divers enviromental conditions
• prepare probe and hybridisize to microarray
• compare data
• do hierarchical clustering
• search for sequence motives

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Two major responses...

• general response
• to environmental changes
• specific responses
• to specific environmental changes

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The general response

• environmental stress response (ESR)
• transient changes in expression patterns
• ESR is a graded response
• initiation of ESR
• - when shifted to less optimal environment
• - by divers Regulators

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The general response

• environmental stress response (ESR)
• transient changes in expression patterns
• ESR is a graded response
• initiation of ESR
• - when shifted to less optimal environment
• - by divers Regulators

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Environmental stress response

• a set of 900 genes (14) displayed a nearly
• identical expression profile in all samples
• one Cluster repressed
• one Cluster induced

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• repressed
• growth-related genes
• genes encoding ribosomal proteins (slightly
  delayed)
• induced
• genes triggering survival in inhospitable
  environments
• differential expression of isoenzymes
• storage of energy reserves
• synthetic and catabolic enzymes

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• repressed
• growth-related genes
• genes encoding ribosomal proteins (slightly
  delayed)
• induced
• genes triggering survival in inhospitable
  environments
• storage of energy reserves
• synthetic and catabolic enzymes
• differential expression of isozymes

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isozymes
possible explanations 1) isozymes with
similar function are regulated by different
pathways 2) isozymes with different
properties are adapted to specific
conditions
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The general response

• environmental stress response (ESR)
• the ESR is a graded and transient response
• initiation of ESR
• - when shifted to less optimal environment
• - by divers Regulators

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transient changes in expression patterns

• stress causes massive and rapid genome-wide
  changes in gene expression which are largely
  transient
• - serving as a loading dose, providing rapid
• but relativly small alternations in protein
• levels
• - correlated change of protein level, playing
• an important role during the transient
  period

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transient changes in expression patterns

• duration and amplitude of the transient change
  vary with the magnitude of the enviromental
  change
• - so induction of ESR may provide a useful
• operational definition of suboptimal
• environments,
• - and can therefore serve as a molecular
• measure of the level of stess experienced
• by the cell.

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transient changes in expression patterns
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The general response

• environmental stress response (ESR)
• transient changes in expression patterns
• ESR is a graded response
• initiation of ESR
• - when shifted to less optimal environment
• - by divers regulators

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Initiation of ESR

• ESR is initiated in response to transitions to
  less optimal environments in contrast to the
  reciprocal change
• - temperature shift 25 --gt 37
• reciprocal shift 37 --gt 25
  (repressed ESR)
• - osmolarity shift hypo --gt hyper
• reciprocal shift hyper --gt hypo (repressed
  ESR)

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Initiation of ESR

• ESR is not governed by one all-purpose regulatory
  system
• - suggested als ESR inducer msn2p, msn4p
• - testing mutants lacking these factors
• provides evidence for alternative
• regulators

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msn2/4p dependence

The shown cluster is dependent on msn2/4p in
response to heat shock but not in response to
H2O2. Because this cluster is induced through
Yap1p in response to H2O2.
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What can we learnfrom microarrays about gene
expression patterns?
http//www-genome.stanford.edu/yeast_stress
presentated by Sonja Prohaska