Gene Regulation in
Eukaryotes
Same basic idea, but more intricate than in
prokaryotes
Why?
1. Genes have to respond to both environmental
and physiological conditions
2. Developmentally triggered genes that organize
cells into tissues, tissues into organs, and
organs into an entire organism
Transcription and translation overlap in prokaryotes
New polypeptides
•RNA polymerase IV synthesizes siRNA in
plants
•RNA polymerase V synthesizes RNAs involved
in siRNA-directed modification of chromatin in
plants
There are many opportunities for regulation of
eukaryotic gene expression!
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Eukaryotic DNA is closely associated with
proteins with the resulting chromatin
structure playing a role in determining which
genes are available for transcription.
Among those genes that are available for
transcription, the presence of proteins referred
to as transcription factors determines which
genes will be transcribed.
Following transcription, processing of the
RNA transcript exerts another level of
regulation.
Transport of the mRNA to the cytoplasm and
its stability in the cytoplasm represent
additional levels of control.
When and how long a protein is active in the
cytoplasm represents a post-translational
level of control.
Gene expression can be regulated by chromatin remodeling!
• DNA that is highly condensed with
histone proteins is referred to as
heterochromatin in contrast to the
more diffuse euchromatin.
• Genes contained in the
heterochromatin regions of a
chromosome are usually not
expressed because the packaging
of DNA into nucleosomes can make
DNA physically inaccessible to RNA
polymerase for transcription.
• In a process called chromatin
remodeling, specialized proteins
can cause the nucleosome forming
histone proteins to disassociate from
the DNA molecule exposing genes
for transcription.
• The presence or absence of
chromatin remodeling proteins
represents an important mechanism
for global regulation of many genes
on large segments of chromosomes.
WT
Chromatin
Remodeling
protein
Gene 1
Gene 1 promoter
Green fluoroscent protein
mutant
Exposing the DNA does not ensure
transcription of its genes!
• To initiate transcription eukaryotic
RNA polymerase requires the
assistance of proteins called
transcription factors.
• Transcription factors are produced
in response to environmental and
developmental signals to elicit an
appropriate change in gene
expression.
• There are additional control
elements on genes which interact
with activators and regulators to
further enhance or otherwise
modify transcription.
• The result is a combination of
factors that form a complex that
determines the rate at which the
RNA polymerase transcribes the
gene.
Eukaryotic Promoter
Site where
other regulatory
proteins bind to
enhance
transcription
Sequence
recognized by
a transcription
factor
A site where regulatory
proteins can bind to
enhance transcription
Sequence where
DNA is denatured
determining where
transcription
starts
Transcription factor binds to
the core promoter region
Different transcription factors bind with the RNA polymerase
This holoenzyme
complex recognizes the
original transcription
factor
Enhancers act as
transcription activators
Can have inhibitors –
negative regulators that
prevent the binding of
the transcription factors
Regulatory proteins are specifically structured to
interact with certain nucleotide sequences on the
DNA molecule.
• The regulation of gene expression
in eukaryotes requires the binding
of specialized proteins to the DNA
molecule.
• Thus far, research has revealed
four kinds of structural motifs for
DNA binding proteins.
• As noted to the right, each type of
binding protein is capable of
activating or inactivating certain
categories of genes (e.g. genes
expressed at certain stages of
development).
• Notice that the structural motifs fit
into the major and minor groves
on the DNA, have amino acids
that fit into the interior of the
double helix, or amino acids that
form hydrogen bonds with bases
inside the DNA molecule.
Environmental responses and developmental changes
requires coordinating the expression of multiple genes
• Recall that in prokaryotes related
genes are linked together in an
operon.
• Eukaryotes do not have operons, but
do have the need to turn on (or off)
groups of genes at the same time.
• This can be accomplished because
groups of related genes have the
same regulator sequences in their
promoter and respond to the same
regulator protein.
• As shown to the right, a regulator
protein produced in response to an
environmental stress interacts with a
stress response element (SRE) in the
promoter of those genes needed for
responding to the stress even though
the genes may be scattered on
different chromosomes throughout
the genome.
• Some of the proteins produced during
developmental changes are
transcription factors which trigger
cascades of expression of
developmental genes.
Stress response proteins
Eukaryotic gene expression can be
regulated after translation!
• There are opportunities to alter the activity of a protein after it is made
by chemical modification (protein processing) as well as by how
quickly the protein itself is degraded (protein degradation).
• With respect to protein degradation, eukaryotic cells can earmark a
protein for destruction by tagging it with a special molecule called
ubiquitin (see below). Once tagged, the ubiquinated protein will enter
a polypeptide shredder called the proteasome. The proteasome
shreds the protein into small peptide fragments that can be further
broken down to component amino acids to be used again to build new
proteins.
Molecular genetics
• Previous discussions focused on the individual.
• Focus has now shifted to genes
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How are they encoded -DNA structure
How do they replicate - DNA replication
How are they expressed - transcription
How are they expressed - translation
Review on these topics (4/12, 4/14)
Relationship between phenotype and genotype - pathways
How are they regulated - Gene regulation
• How we study them - individual genes (4/23, 4/26)
• Review on pathways, gene regulation and recombinant DNA (4/28)
• Exam IV (4/30)
• How we study them - global studies (Genomics-4/26, 5/3, 5/5)
• Final Exam 5/10