Transcript Gene expression - Weizmann Institute of Science

GENE EXPRESSION:
(EUCARYOTIC)
•GENE =SEGMENT OF DNA = BLUEPRINT FOR A
SINGLE PROTEIN
•EACH CELL CONTAINS ALL GENES !!!
•WHEN A GENE IS EXPRESSED, THE PROTEIN IT
CODES FOR IS SYNTHESIZED (AT RIBOSOMES)
•NOT ALL GENES ARE EXPRESSED IN ALL CELLS (OF A
MULTICELLULAR ORGANISM) OR AT ALL TIMES
DIFFERENTIATION
• DIFFERENT CELL TYPES SYNTHESIZE DIFFERENT PROTEINS
• TYPICAL HUMAN CELL – ABOUT 10-20,000 EXPRESSED GENES
• FOR THE 2000 MOST ABUNDANT (>50,000 COPIES/CELL)
FEW DIFFERENCES ARE FOUND (5 FOLD OR LESS)
• A FEW % ARE CELL TYPE SPECIFIC – BUT PROFILES DO
DIFFER SIGNIFICANTLY
A PARTICULAR CELL’S EXPRESSED GENES VARY
•WITH TIME
•IN RESPONSE TO EXTERNAL SIGNALS
•IN RESPONSE TO INTERNAL “CLOCKS”
•DEPENDING ON STATE – NORMAL, STRESSED, ABNORMAL
HOW IS GENE EXPRESSION REGULATED??
TRANSCRIPTION
M-RNA IS PROCESSED
(SPLICED)
REGULATION AT DIFFERENT STEPS
mRNA IS PROCESSED
(SPLICED)
PREVALENT (NO SYNTHESIS)
TRANSCRIPTIONAL CONTROL
RNA PROCESSING CONTROL
RNA TRANSPORT CONTROL
TRANSLATIONAL CONTROL
RNA DEGRADATION
PROTEIN ACTIVITY
TRANSCRIPTION – CLOSER LOOK
RNA POLYMERASE
ATTACHES TO DNA, MOVES
ALONG IT, OPENS DOUBLE HELIX, SYNTHESIZES mRNA.
CONTROL OF EXPRESSION BY ASSISTING OR BLOCKING
ATTACHMENT OF RNA POLYMERASE TO DNA.
RNA POLYMERASE BINDS AT A SPECIFIC REGION, THE
PROMOTER, AT THE START OF THE GENE, IF (1) AN
ACTIVATOR
IS ATTACHED AT AN ADJACENT SPECIFIC
REGULATORY BINDING SEQUENCE (OPERATOR) AND (2) A
REPRESSOR
IS NOT ATTACHED TO ITS OWN OPERATOR
TRANSCRIPTION START
TRANSCRIPTION – CLOSER LOOK
RNA POLYMERASE DOES NOT BIND AT THE
PROMOTER, AT THE START OF THE GENE, IF A
REPRESSOR
IS ATTACHED TO IT’S OWN OPERATOR
TRANSCRIPTION
FACTORS
RECOGNITION OF BINDING MOTIFS IN DNA
RECOGNITION OF BINDING MOTIFS IN DNA 2
HOMEODOMAIN
TRYPTOPHAN REPRESSOR-SWITCH
REGULATORY
“NETWORK”
Trp(P)
OPERON
Enzymes(G)
repressor(P)
lac OPERON – E-COLI (PROCARYOTIC)
OPERON – SET OF GENES PLACED ONE AFTER THE OTHER
ON DNA, TAKING PART IN ONE PROCESS (BREAKDOWN OF
lactose). E-COLI PREFERS glucose – WILL PROCESS lactose
ONLY UNDER ( –glucose/+ lactose ) CONDITIONS. 4-SWITCH!
Cyclic AMP
allolactose
CONCENTRATION
CONCENTRATION
ACTIVATOR:
REPRESSOR:
--glucose/+lactose
+
+
WHEN +glucose
WHEN +lactose
(ACTIVE IF COMPLEX)
(ACTIVE IF FREE)
Decision-making by bacteria: choosing between two sugars can be tough…
The first detailed map of a gene’s decision-making computation (Setty, Alon, 2003)
EUCARYOTIC – MUCH MORE COMPLEX
• RNA POLYMERASE CANNOT INITIATE TRANSCRIPTION
GENERAL TRANSCRIPTION FACTORS ASSEMBLE, FORM
COMPLEX ON OPERATOR NEAR PROMOTER - ABUNDANT
TBP – SUBUNIT OF TFIID
• SPECIFIC REGULATORS OF TRANSCRIPTION (ENHANCERS)
CAN ATTACH TO DNA MANY 1000 OF BP UPSTREAM,
CAN EVEN BE PLACED DOWNSTREAM FROM START SITE
VERY MINUTE AMOUNT PRESENT
• MAY NEED MORE THAN ONE TRANSCRIPTION FACTOR TO
ACTIVATE GENE
proximity of GAL4
enhances 1000 fold
the attachment of
TFIIB to TFIID
control of human beta-globin
REGULATORY NETWORKS
• TRANSCRIPTION FACTORS ARE PROTEINS THAT
ACTIVATE OR REPRESS GENES’ TRANSCRIPTION INTO
PROTEINS
• PROTEINS FORM COMPLEXES THAT INDUCE /TURN OFF
/REGULATE A GENE’S TRANSCRIPTIONAL CAPACITY
COMPLEX NETWORKS OF REGULATION OF GENE
EXPRESSION EMERGE
HANAHAN & WEINBERG
CELL 2000
CANCER IS CAUSED BY THE BREAKDOWN OF SEVERAL
IMPORTANT NETWORKS,THAT GUARD AGAINST
UNCONTROLLED PROLIFERATION
NORMAL CELL STATES & CELL CYCLE
G1 –gap, decide whether to proliferate, wait
or cross to non-dividing stage G0
S -- DNA Synthesis
G2– gap, allow DNA repair
M – Mitosis, cell division
Check Points (Internal and External signals)
NORMAL ENTRY TO/EXIT FROM CELL
CYCLE
Programmed
Cell Death
(Apoptosis)
Induced Apoptosis
Growth Signals
Cell Division
Proliferation
Limited replication,
senescence, crisis
too many divisions
Cell cycle arrest (G0) or
Terminal differentiation
Anti Growth Signals
Check Point (Internal and External signals)
Cancer Cell-HALLMARKS
series of random genetic accidents
Programmed
Cell Death
(Apoptosis)
3
Cell Division
Proliferation
Limited replication,
senescence, crisis
3
4
2
1
Cell cycle arrest or
Terminal differentiation
Defective computation at check points, or failure to
interpret signals or execute instructions:
1 Proliferation becomes independent of growth factors.
2 Loosing responses to cell cycle inhibitory signals.
3 Failure to apoptose when necessary.
4 Immortalization.
These are the main 4 HALLMARKS OF CANCER.
1. SELF SUFFICIENCY IN GROWTH SIGNALS
IN NORMAL CELLS, GROWTH FACTORS ARE RELEASED
BY NEIGHBOR CELLS, BOUND BY GF RECEPTORS (USUALLY
IN CELL MEMBRANE), WHICH GET MODIFIED AND INITIATE
A CASCADE OF SIGNALING EVENTS .
What can go wrong?
1. Autonomous generation of growth factors
2. Receptor overexpression or alteration
3. Defective downstream processing
MUTANT Ras SEND DOWNSTREAM GROWTH SIGNALS WITH
NO STIMULUS FROM UPSTREAM
2. IGNORING ANTI-GROWTH SIGNALS
IN NORMAL CELLS, MOST ANTIGROWTH SIGNALS DIRECTING
THE CELL TO G0 ARE CHANNELED THROUGH THE Rb
(RETINOBLASTOMA) PROTEIN.
TERMINAL DIFFERENTIATION IS INDUCED BY FORMATION
OF Myc-Max COMPLEX.
3. EVADING APOPTOSIS
THE APOPTOTIC MACHINERY RELIES ON SENSORS (THAT
DETECT INTERNAL AND EXTERNAL SIGNALS) AND
EFFECTORS, THAT INDUCE AND CARRY OUT THE DEATH
SENTENCE. p53 IS A CENTRAL PLAYER IN APOPTOSIS.
4. IMMORTALIZATION
A CELL CAN UNDERGO A LIMITED NUMBER OF DIVISIONS.
THE “COUNTING DEVICE” IS A STRING OF SEVERAL 1000
REPEATS OF A 6-BP SEQUENCE ELEMENT AT THE END OF
THE CHROMOSOMES (TELOMERS). IN EACH DIVISION 50 –
100 TELOMERIC BP ARE LOST. WHEN THEY RUN OUT, THE
CHROMOSOME ENDS ARE UNPROTECTED AND FUSE,
LEADING TO CRISIS AND DEATH OF THE CELL.
CANCER CELLS ACQUIRE TELOMERE MAINTENANCE
Cancer Cell-HALLMARKS
series of random genetic accidents
Programmed
Cell Death
(Apoptosis)
3
Cell Division
Proliferation
Limited replication,
senescence, crisis
3
4
2
1
Cell cycle arrest or
Terminal differentiation
Defective computation at check points, or failure to
interpret signals or execute instructions:
1 Proliferation becomes independent of growth factors.
2 Loosing responses to cell cycle inhibitory signals.
3 Failure to apoptose when necessary.
4 Immortalization.
These are the main 4 HALLMARKS OF CANCER.
TWO MORE:
5. Formation of new blood vessels in the tumor (Sustained Angiogenesis)
(NEEDED TO ACHIEVE LARGE SIZE)
6. Acquirement of metastatic behavior (cancer cells spread to vital organs)
(CAUSE OF 90% OF CANCER RELATED DEATHS)
Cancer results from anomalies in
genes regulating cell growth:
mutations, translocations
• Two classes of genes are involved:
• 1) Oncogenes - positive regulators
promote cancer by hyperactivity (one allele
is enough)
• 2) Tumor Suppressor genes - negative
regulators, promote cancer by loss of
activity (both alleles must be mutated)
AND/OR GENOMIC INSTABILITY:
SCIENCE 2002
GENES
ONCOGENES = GAS PEDAL
TUMOR SUPPRESSORS = BRAKE PEDAL
GENOME INTEGRITY GENES = MECHANIC
AIMS:
UNDERSTAND THE GENETIC/MOLECULAR MECHANISMS
THAT CAUSE CANCER.
WHICH PATHWAYS BREAK DOWN IN VARIOUS CANCERS,
AND HOW?
IDENTIFY SUB-CLASSES OF EACH DISEASE.
CLINICAL RELEVANCE:
PERSONALIZED PREDICTIVE PREVENTIVE MEDICINE:
PREDICT OUTCOME, DESIGN SUITABLE THERAPY
DRUG DISCOVERY
MLL translocations specify a
distinct gene expression
profile that distinguishes a
unique leukemia
Armstrong et al, Nature Genetics
30, 41-47 (2002)
PCA Leukemia 2
Korsmeyer
ALL,AML,MLL
500 most separating
genes
GLEEVEC IN CML: