Transcript 33_eukaryote1

32 Gene regulation in
Eukaryotes
Lecture Outline 11/28/05
• Gene regulation in eukaryotes
– Chromatin remodeling
– More kinds of control elements
• Promoters, Enhancers, and Silencers
• Combinatorial control
• Cell-specific transcription
– Post transcription gene regulation
• mRNA processing
• Micro RNAs
• Protein degradation
– Differentiation and Development
• A cascade of transcription regulators
• Examples from flowers and fruit flies
Gene Regulation in
Prokaryotes and Eukarykotes
• Prokaryotes
– Operons
• 27% of E. coli genes
• (Housekeeping genes
not in operons)
– simultaneous
transcription and
translation
• Eukaryotes
– No operons, but they still
need to coordinate
regulation
– More kinds of control
elements
– RNA processing
– Chromatin remodeling
• Histones must be modified
to loosen DNA
– Short- and long-term
regulation
Signal
NUCLEUS
Chromatin
modification:
DNA
Gene
Transcription
RNA
RNA processing
Transport to cytoplasm
CYTOPLASM
Degradation
of mRNA
Polypetide
Translation
Cleavage
Chemical modification
Transport to cellular destination
Active protein
Degradation of protein
Figure 19.3
Degraded protein
DNA Packing
30 nm
Nucleosome
(b) 30-nm fiber
Protein scaffold
Loops
300 nm
(c) Looped domains (300-nm fiber)
700 nm
1,400 nm
Figure 19.2
Scaffold
Histone Modification
Chromatin changes
Transcription
RNA processing
mRNA
Translation
degradation
Protein processing
and degradation
DNA
double helix
Figure 19.4a
Histone
tails
Amino acids
available
for chemical
modification
Histone acetylation loosens
DNA to allow transcription
Unacetylated histones
Figure 19.4 b
Acetylated histones
Densely packed chromatin
Activator recruits chromatin remodeling and acetylation proteins
RNA Pol
Transcription
http://cats.med.uvm.edu
Review transcription in
Eukarkyotes
Enhancer
(distal control elements)
Poly-A signal
sequence
Proximal
control elements
Exon
Intron
Exon
Intron
Termination
region
Exon
DNA
Downstream
Upstream
Promoter
Chromatin changes
Transcription
Exon
Primary RNA
5
transcript
(pre-mRNA)
Intron
mRNA
degradation
Intron RNA
Exon
Cleared 3 end
of primary
transport
Coding segment
Translation
Protein processing
and degradation
Intron
RNA processing:
Cap and tail added;
introns excised and
exons spliced together
Transcription
RNA processing
Exon
Poly-A
signal
mRNA
G
P
P
5 Cap
P
5 UTR
(untranslated
region)
Start
codon
Stop
codon
Poly-A
3 UTR
(untranslated tail
region)
Many components
must be assembled to
initiate transcription
Those common
components are called
“General Transcription
Factors”
There are also many other
transcription factors that control
transcription of particular genes in
particular conditions
Control of Galactose
metabolism in yeast
Two Repressor proteins bind to
control region
Control of Galactose
metabolism in yeast
Galactose can bind to repressor
complex. Opens activation site
to stimulate transcription
Enhancers and activators
Distal control
element
Activators
Enhancer
Promoter
Gene
TATA
box
Activator proteins bind
to distal control elements.
1
General
transcription
factors
DNA-bending
protein
Group of
Mediator proteins
2
A DNA-bending protein
brings the bound activators
closer to the promoter.
3
The activators bind to
certain general transcription
factors and mediator
proteins.
Fig 19.5
RNA
Polymerase II
Chromatin changes
Transcription
RNA processing
mRNA
degradation
RNA
Polymerase II
Translation
Protein processing
and degradation
Transcription
Initiation complex
RNA synthesis
Transcriptional synergy
• Combinations of different enhancers
affect the strength of transcription
How eukaryotic gene repressors can function:
Cell type–specific transcription
Enhancer
Promoter
Albumin gene
All cells have the
same genes, but
only certain
genes are
expressed in
each tissue
Control
elements
Crystallin gene
Liver cell
nucleus
Lens cell
nucleus
Liver cell
Lens cell
Albumin gene
expressed
Fig 19.7
Different set of
activator proteins
in the two cell
types
Crystallin gene
not expressed
Albumin gene
not expressed
Crystallin gene
expressed
Long-term control of transcription:
methylation
• Certain cytosine bases can be
methylated, which blocks transcription
– Usually CG dinucleotides
– Recruits proteins which deacetylate
histones, inactivating nearby genes
Genomic imprinting:
inactivation of maternal or paternal genes
Some
alleles are
tagged by
methyl C.
Signal
NUCLEUS
Post-transcription
control of gene
expression
Chromatin
modification:
DNA
Gene
Transcription
RNA
RNA processing
Transport to cytoplasm
CYTOPLASM
Degradation
of mRNA
Translation
Polypetide
Active protein
Degradation of protein
Degraded protein
Alternative RNA splicing
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Exons
DNA
Primary
RNA
transcript
RNA splicing
mRNA
Fig 19.8
or
Micro-RNAs
3 One strand
Dicer cuts
The micro- dsRNA into
of miRNA
RNA (miRNA) short segments associates with
precursor folds
protein.
back on itself
1
2
The bound
miRNA can basepair with any
complementary
mRNA
4
5
Prevents gene
expresion
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Protein
complex
Translation
Protein processing
and degradation
Dicer
Degradation of mRNA
OR
miRNA
Target mRNA
Hydrogen
bond
Fig 19.9
Blockage of translation
Degradation of a protein by a
proteasome
1
Chromatin changes
Ubiquitin molecules
are attached to a
protein
The ubiquitin-tagged
protein is recognized
by a proteasome.
2
3
The proteasome
cuts the protein into
small peptides.
Transcription
RNA processing
Ubiquitin
mRNA
degradation
Translation
Proteasome
Proteasome
and ubiquitin
to be recycled
Protein processing
and degradation
Protein to
be degraded
Fig 19.10
Ubiquinated
protein
Protein entering a
proteasome
Protein
fragments
(peptides)
Development
Mutant Drosophila with an
extra small eye on its
antenna
Figure 21.1
Determination and differentiation of muscle cells
Nucleus
myoD
Other muscle-specific genes
DNA
OFF
Embryonic
precursor cell
OFF
1 Determination. Signals from
OFF
myoD is a “master control”
gene: it makes
a
mRNA
transcription factor that can activate other
The cell is now
protein
ireversibly
muscle specific genes. MyoD
(transcription factor)
other cells activate a master
regulatory gene, myoD,
Myoblast
(determined)
2
determined
Differentiation. MyoD
protein activates
other muscle-specific
transcription factors, which
in turn activate genes for
muscle proteins.
The embryonic precursor
cell is still undifferentiated
mRNA
MyoD
Muscle cell
(fully differentiated)
Fig 21.10
The cell is now fully
differentiated
mRNA
Another
transcription
factor
mRNA
mRNA
Myosin, other
muscle proteins,
and cell-cycle
blocking proteins
Determination and differentiation of muscle cells
Nucleus
Master control gene myoD
Other muscle-specific genes
DNA
OFF
Embryonic
precursor cell
1
Myoblast
(determined)
2
Determination.
Signals from other
cells activate a
master regulatory
gene, myoD,
Differentiation. MyoD
protein activates
other muscle-specific
transcription factors, which
in turn activate genes for
muscle proteins.
OFF
OFF
mRNA
MyoD protein
(transcription factor)
mRNA
MyoD
Muscle cell
(fully differentiated)
Fig 21.10
The cell is now fully
differentiated
mRNA
Another
transcription
factor
The cell is now
ireversibly
determined to
become a
muscle cell.
mRNA
mRNA
Myosin, other
muscle proteins,
and cell-cycle
blocking proteins
Determination and differentiation of muscle cells
Nucleus
Master control gene myoD
Other muscle-specific genes
DNA
OFF
Embryonic
precursor cell
OFF
1 Determination. Signals from
other cells activate a master
regulatory gene, myoD,
MyoD protein
(transcription factor)
Myoblast
(determined)
2
OFF
mRNA
Differentiation. MyoD
protein activates
other muscle-specific
transcription factors, which
in turn activate genes for
muscle proteins.
mRNA
MyoD
Muscle cell
(fully differentiated)
Fig 21.10
The cell is now fully
differentiated
mRNA
Another
transcription
factor
The cell is now
ireversibly
determined
mRNA
mRNA
Myosin, other
muscle proteins,
and cell-cycle
blocking proteins
Genetic control of Flower
Development
Normal
Flower
“ABC Model”
Apetala
Class A
Pistillata
Class B
Agamous
Class C
These genes all code for transcription factors
The effect of the bicoid gene, an egg-polarity gene in
Drosophila
Tail
Head
T1
T2
T3
A1 A2 A3 A4 A5
A6 A7
A8
Normal larva
Tail
Tail
Figure 21.14
A8
A8
A7
A6
A7
Mutant larva (bicoid)
A mutation in bicoid leads to tail structures at both ends
(bottom larva).
Hierarchy of Gene Activity in Early Drosophila Development
Maternal effect genes (egg-polarity genes)
Gap genes
Pair-rule genes
Segment polarity genes
Homeotic genes of the embryo
Other genes of the embryo
Segmentation genes
of the embryo
Drosophila pattern formation
Nurse cells
Egg cell
1 Developing
egg cell
bicoid mRNA
2 Bicoid mRNA
in mature
unfertilized egg
Fertilization
Translation of bicoid mRNA
100 µm
3 Bicoid protein in
early embryo
Anterior end
(b) Gradients of bicoid mRNA and bicoid protein in normal egg and early embryo.
Homeotic genes
Homeotic genes
• Regulatory
genes that
control organ
identity
• Conserved
from flies to
mammals