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CHAPTER 19
Control of
Eukaryotic Genes
“Epigenetics”
2007-2008
The BIG Questions…
• How are genes turned on & off
in eukaryotes?
• How do cells with the same genes
differentiate to perform completely
different, specialized functions?
REVIEW
Evolution of gene regulation
• Prokaryotes
– single-celled
– evolved to grow & divide rapidly
– must respond quickly to changes in external
environment
• exploit transient resources
• Gene regulation = (?) Operons
– turn genes on & off rapidly
• flexibility & reversibility
– adjust levels of enzymes
for synthesis & digestion
Evolution of gene regulation
• Eukaryotes
– Multicellular = only expresses a fraction of its genes
– evolved to maintain constant internal
conditions even with changing conditions
• (?) Homeostasis
• must REGULATE the body as a whole rather than
serve the needs of individual cells
– Also need to regulate:
• (?) growth & development
–long term processes
• (?) specialization
–turn on & off large number of genes
Points of control
• 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
Structural Organization
• Chromatin is packed into chromosomes
=ordered into higher structural levels
compared to prokaryotes
Figure 19.1
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1. DNA packing as gene control
– Unfolded chromatin has the appearance
of beads on a string
• Each “bead” is a (?) nucleosome
– Made up of (?) histones
2 nm
DNA double helix
Histones
Histone
tails
Histone H1
Linker DNA
(“string”)
Nucleosome
(“bead”)
(a) Nucleosomes (10-nm fiber)
Figure 19.2 a
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10 nm
2. Where does transcription occur on chromosome
• Degree of packing of DNA regulates transcription
– If tightly wrapped around histones
= (?) no transcription
= (?) genes turned off
 heterochromatin
darker DNA (H) = tightly packed
 euchromatin
lighter DNA (E) = loosely packed
H
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E
Higher Levels of DNA Packing
• The next level of packing
– Forms the 30-nm chromatin fiber
30 nm
Nucleosome
(b) 30-nm fiber
Figure 19.2 b
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• The 30-nm fiber, in turn
– Forms looped domains, making up a 300-nm
fiber
Protein scaffold
Loops
300 nm
(c) Looped domains (300-nm fiber)
Figure 19.2 c
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Scaffold
• In a mitotic chromosome
– The looped domains coil and fold
= metaphase chromosome
700 nm
1,400 nm
(d) Metaphase chromosome
Figure 19.2 d
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What regulates Chromatin Structure ?

Acetylation of histones (?) unwinds DNA
 (?) attachment of acetyl groups (–COCH3)
(?) enables transcription
 (?) genes turned on
 transcription factors have easier access to genes

Unacetylated histones
Figure 19.4 b
Acetylated histones
(b) Acetylation of histone tails promotes loose chromatin structure that
permits transcription
DNA methylation
• Methylation of DNA (?) blocks transcription factors
– (?) attachment of methyl groups (–CH3) to cytosine
 (?) genes turned off
– nearly permanent inactivation of genes
• ex. inactivated mammalian X chromosome = Barr body
Epigenetic Inheritence
=Terminology for gene expression
- ** DNA sequence NOT changed, just the expression
of the gene (on or off)
- Can Chromatin modifications be passed offspring?
(sometimes – poorly understood)
**** In
a new embryo, all tags are removed except for
“imprinted” tags for getting development started
Examples of “epigenetics”
• Morphogenesis and specialization
Examples of “epigenetics”
• FTO gene & obesity
Cytogenetic Location: 16q12.2
Molecular Location on chromosome 16: base pairs
53,703,962 to 54,114,466
Examples of “epigenetics”
• Cancer
Examples of “epigenetics”
• Twin Studies…”epigenetic drift”
•
http://learn.genetics.utah.edu/content/epigenetics/twins/
III. PROCESS CONTROLS
– (?) transcription controls seem to
be the most “important” factor in
gene expression
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A. The Roles of Transcription Factors
• To initiate transcription
– (?) RNA polymerase requires transcription
factors (proteins) to bind to the
(?) promotor region
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B. Role of Enhancers
–enhancer
• DNA sequence (?) upstream from
promotor
• Activator protein – “enhance” (high
level) or transcription
Model for Enhancer action
• Enhancer DNA sequences
– (?) distant control
sequences
• Activator proteins
– (?) bind to enhancer
sequence & stimulates
transcription
• Repressor proteins
• bind to enhancer sequence &
(?)block gene transcription
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Transcription complex
Activator Proteins
• regulatory proteins bind to DNA at distant
Enhancer Sites
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
C. Significance of protein-mediated bending
• Activators BEND TOWARD transcription factors
stimulating transcription (influence chromatin structure)
Distal control
element
Activators
Enhancer
1 Activator proteins bind
to distal control elements
grouped as an enhancer in
the DNA. This enhancer has
three binding sites.
2 A DNA-bending protein
brings the bound activators
closer to the promoter.
Other transcription factors,
mediator proteins, and RNA
polymerase are nearby.
Promoter
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
Mediator proteins
RNA
Polymerase II
Chromatin changes
3 The activators bind to
certain general transcription
factors and mediator
proteins, helping them form
an active transcription
initiation complex on the promoter.
Transcription
RNA processing
mRNA
degradation
Figure 19.6
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RNA
Polymerase II
Translation
Protein processing
and degradation
Transcription
Initiation complex
RNA synthesis
2. Post-transcriptional controls
= RNA modification
* Gene expression can be blocked or stimulated
during RNA modification
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A. Role of RNA Processing
– (?) exons joined after introns cut out
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Exons
DNA
Primary
RNA
transcript
RNA splicing
Figure 19.8
mRNA
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or
B. Role of mRNA Degradation
• The life span of mRNA molecules in the
cytoplasm (hours to weeks)
– Degradation of the leader (5’cap) and trailer
regions (poly-A tail) by enzymes
– Prokaryotes vs. Eukaryotes lifespan
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3. Translation Control
• (?) Regulatory proteins – attach to 5’ end of
mRNA
– Prevent attachment of ribosome
– Block translation
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B. Protein Processing
• After translation
– (?)protein processing/modification are
controlled by cellular events (Endo. System)
= folding, cleaving, adding sugar groups,
targeting for transport
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Protein degradation (Figure 19.10)
• Ubiquitin tagging
• Proteasomes
3 Enzymatic components of the
Chromatin changes
Transcription
1 Multiple ubiquitin molecules are attached to a protein
by enzymes in the cytosol.
2 The ubiquitin-tagged protein
is recognized by a proteasome,
which unfolds the protein and
sequesters it within a central cavity.
proteasome cut the protein into
small peptides, which can be
further degraded by other
enzymes in the cytosol.
RNA processing
mRNA
degradation
Proteasome
and ubiquitin
to be recycled
Ubiquitin
Translation
Proteasome
Protein processing
and degradation
Protein to
be degraded
Ubiquinated
protein
Figure 19.10
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Protein
fragments
(peptides)
Protein entering a
proteasome
Ubiquitin
1980s | 2004
• “Death tag”
– mark unwanted proteins with a label
– 76 amino acid polypeptide = ubiquitin
– labeled proteins are broken down rapidly in
"waste disposers“ = proteasomes
Nobel Prize 2004
Aaron Ciechanover
Israel
Avram Hershko
Israel
Irwin Rose
UC Riverside
Proteasome
• (?) Protein-degrading “machine”
– cell’s waste disposer
– breaks down any proteins
into 7-9 amino acid fragments
• cellular recycling
play Nobel animation
RNA interference
• Small interfering RNAs (siRNA)
– short segments of RNA (21-28 bases)
• bind to mRNA
• create sections of double-stranded mRNA
• “death” tag for mRNA
– triggers degradation of mRNA
– causes (?) gene “silencing”
siRNA
• post-transcriptional control
• (?) turns off gene = no protein produced
Nobel Prize 2006
UMASS!!!
Action of siRNA
dicer
enzyme
mRNA for translation
siRNA
double-stranded
miRNA + siRNA
breakdown
enzyme
(RISC)
mRNA degraded
functionally turns
gene off
• Now that the complete sequence of the human
genome is available
– 98.5% does not code for proteins, rRNAs, or
tRNAs
Exons (regions of genes coding
for protein, rRNA, tRNA) (1.5%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Alu elements
(10%)
Figure 19.14
Simple sequence
DNA (3%)
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Repetitive
DNA
unrelated to
transposable
elements
(about 15%)
Introns and
regulatory
sequences
(24%)
Unique
noncoding
DNA (15%)
Large-segment
duplications (5-6%)
Another post-transcriptional control….
• RNAi RNA interference by microRNAs (miRNAs)
– Can lead to degradation of an mRNA or block its
translation
1 The microRNA (miRNA)
precursor folds
back on itself,
held together
by hydrogen
bonds.
22 An enzyme
called Dicer moves
along the doublestranded RNA,
cutting it into
shorter segments.
3 One strand of
each short doublestranded RNA is
degraded; the other
strand (miRNA) then
associates with a
complex of proteins.
4 The bound
miRNA can base-pair
with any target
mRNA that contains
the complementary
sequence.
55 The miRNA-protein
complex prevents gene
expression either by
degrading the target
mRNA or by blocking
its translation.
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Protein
complex
Dicer
Degradation of mRNA
OR
miRNA
Target mRNA
Figure 19.9
Hydrogen
bond
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Blockage of translation