Transcript Regulation of gene e

Control of
Eukaryotic Genes
AP Biology
2007-2008
The BIG Questions…
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How are genes turned on & off
in eukaryotes?
How do cells with the same genes
differentiate to perform completely
different, specialized functions?
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Evolution of gene regulation
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Prokaryotes
single-celled
 evolved to grow & divide rapidly
 must respond quickly to changes in
external environment
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exploit transient resources
Gene regulation
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turn genes on & off rapidly
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flexibility & reversibility
adjust levels of enzymes
for synthesis & digestion
Evolution of gene regulation
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Eukaryotes
multicellular
 evolved to maintain constant internal
conditions while facing changing
external conditions
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homeostasis
regulate body as a whole
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growth & development
 long term processes
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specialization
 turn on & off large number of genes
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must coordinate the body as a whole rather
than serve the needs of individual cells
Points of control
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The control of gene
expression can occur at any
step in the pathway from
gene to functional protein
1. packing/unpacking DNA
2. transcription
3. mRNA processing
4. mRNA transport
5. translation
6. protein processing
7. protein degradation
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1. DNA packing
How do you fit all
that DNA into
nucleus?
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DNA coiling &
folding
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double helix
nucleosomes
chromatin fiber
looped
domains
chromosome
from DNA double helix to
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condensed
Nucleosomes
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8 histone
molecules
“Beads on a string”
1st level of DNA packing
 histone proteins
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8 protein molecules
positively charged amino acids
bind tightly to negatively charged DNA
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DNA
packing movie
DNA packing as gene control
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Degree of packing of DNA regulates transcription
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tightly wrapped around histones
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no transcription
genes turned off
 heterochromatin
darker DNA (H) = tightly packed
 euchromatin
lighter DNA (E) = loosely packed
H
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E
DNA methylation
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Methylation of DNA blocks transcription factors
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no transcription
 genes turned off
attachment of methyl groups (–CH3) to cytosine
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nearly permanent inactivation of genes
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C = cytosine
ex. inactivated mammalian X chromosome = Barr body
Histone acetylation
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Acetylation of histones unwinds DNA
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loosely wrapped around histones
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attachment of acetyl groups (–COCH3) to histones
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enables transcription
genes turned on
conformational change in histone proteins
transcription factors have easier access to genes
Histone Modifications
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In histone acetylation, acetyl groups are
attached to positively charged lysines in
histone tails
This process loosens chromatin structure,
thereby promoting the initiation of
transcription
The addition of methyl groups (methylation)
can condense chromatin; the addition of
phosphate groups (phosphorylation) next
to a methylated amino acid can loosen
Animation: DNA Packing
chromatin
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2. Transcription initiation
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Control regions on DNA
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promoter
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enhancer
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nearby control sequence on DNA
binding of RNA polymerase & transcription
factors
“base” rate of transcription
distant control
sequences on DNA
binding of activator
proteins
“enhanced” rate (high level)
of transcription
Model for Enhancer action
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Enhancer DNA sequences
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Activator proteins
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distant control sequences
bind to enhancer sequence
& stimulates transcription
Silencer proteins
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bind to enhancer sequence
& block gene transcription
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Turning
on Gene movie
Transcription complex
Activator Proteins
• regulatory proteins bind to DNA at
Enhancer Sites
distant enhancer sites
• increase the rate of transcription
regulatory sites on DNA
distant from gene
Enhancer
Activator
Activator
Activator
Coactivator
A
E
F
B
TFIID
RNA polymerase II
H
Core promoter
and initiation complex
Initiation Complex at Promoter Site binding site of RNA polymerase
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An activator is a protein that binds to an
enhancer and stimulates transcription of a
gene
Bound activators cause mediator proteins
to interact with proteins at the promoter
Animation: Initiation of Transcription
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3. Post-transcriptional control
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Alternative RNA splicing
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variable processing of exons creates a
family of proteins
4. Regulation of mRNA degradation
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Life span of mRNA determines amount
of protein synthesis
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mRNA can last from hours to weeks
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RNA
processing movie
mRNA Degradation
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The life span of mRNA molecules in the
cytoplasm is a key to determining protein
synthesis
Eukaryotic mRNA is more long lived than
prokaryotic mRNA
The mRNA life span is determined in part by
sequences in the leader and trailer regions
Animation: mRNA Degradation
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RNA interference
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Small interfering RNAs (siRNA)
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short segments of RNA (21-28 bases)
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bind to mRNA
create sections of double-stranded mRNA
“death” tag for mRNA
 triggers degradation of mRNA
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cause gene “silencing”
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post-transcriptional control
turns off gene = no protein produced
siRNA
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Action of siRNA
dicer
enzyme
mRNA for translation
siRNA
double-stranded
miRNA + siRNA
breakdown
enzyme
(RISC)
mRNA degraded
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functionally
turns gene off
RNA interference
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTi me™ a nd a
TIFF (Uncompre ssed ) decomp resso r
are need ed to se e th is p icture.
Andrew
Fire
AP
Biology
Stanford
QuickTi me™ a nd a
TIFF (Uncompre ssed ) decomp resso r
are need ed to se e th is p icture.
Craig Mello
U Mass
1990s | 2006
“for their discovery of
RNA interference —
gene silencing by
double-stranded RNA”
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
5. Control of translation
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Block initiation of translation stage
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regulatory proteins attach to 5' end of mRNA
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prevent attachment of ribosomal subunits &
initiator tRNA
block translation of mRNA to protein
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Control
of translation movie
Initiation of Translation
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The initiation of translation of selected
mRNAs can be blocked by regulatory
proteins that bind to sequences or
structures of the mRNA
Alternatively, translation of all mRNAs
in a cell may be regulated simultaneously
For example, translation initiation factors
are simultaneously activated in an egg
following fertilization
Animation: Blocking Translation
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6-7. Protein processing & degradation
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Protein processing
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folding, cleaving, adding sugar groups,
targeting for transport
Protein degradation
ubiquitin tagging
 proteasome degradation
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Protein
processing movie
1980s | 2004
Ubiquitin
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“Death tag”
mark unwanted proteins with a label
 76 amino acid polypeptide, ubiquitin
 labeled proteins are broken down
rapidly in "waste disposers"
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AP
proteasomes
Aaron Ciechanover
Biology Israel
Avram Hershko
Israel
Irwin Rose
UC Riverside
Protein Processing and Degradation
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After translation, various types of protein
processing, including cleavage and the
addition of chemical groups, are subject to
control
Proteasomes are giant protein complexes
that bind protein molecules and degrade
them
Animation: Protein Processing
Animation: Protein Degradation
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Proteasome
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Protein-degrading “machine”
cell’s waste disposer
 breaks down any proteins
into 7-9 amino acid fragments
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cellular recycling
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play
Nobel animation
6
7
Gene Regulation
protein
processing &
degradation
1 & 2. transcription
- DNA packing
- transcription factors
5
4
initiation of
translation
mRNA
processing
3 & 4. post-transcription
- mRNA processing
- splicing
- 5’ cap & poly-A tail
- breakdown by siRNA
5. translation
- block start of
translation
1 2
initiation of
transcription
AP Biology mRNA splicing
3
6 & 7. post-translation
- protein processing
- protein degradation
4
mRNA
protection
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The other important source of
developmental information is the
environment around the cell, especially
signals from nearby embryonic cells
In the process called induction, signal
molecules from embryonic cells cause
transcriptional changes in nearby target
cells
Thus, interactions between cells induce
differentiation of specialized cell types
Animation: Cell Signaling
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Axis Establishment
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Maternal effect genes encode for
cytoplasmic determinants that initially
establish the axes of the body of Drosophila
These maternal effect genes are also called
egg-polarity genes because they control
orientation of the egg and consequently the
fly
Animation: Development of Head-Tail Axis in Fruit Flies
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Turn your
Question Genes on!
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2007-2008
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Gene Regulation
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