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Regulation of eukaryotic gene

expression
Sadava: 16.3
16 3 Regulation of eukaryotic genes;
16.4 Epigenetic changes; 16.5 Regulation
after transcription

Eukaryotic Transcription
Eukaryotic genes are encoded by exons interspersed
by introns.
In Eukaryotes,the
Eukaryotes the primary transcript is processed by
adding a 5cap, a 3polyA sequence and removal of
introns ((byy splicing).
p
g)
In Eukaryotes, more than 1 protein product can be
made by 1 eukaryotic gene through a process of
alternative
lt
ti splicing
li i off exons.
In addition to the promoter site(s) there are enhancer
sites (far
( far upstream) for activators to bind; regulation
by repressors and activators is more complex than in
prokaryotes

Figure 16.13 Potential Points for the Regulation of Gene Expression

Gene expression
G
i can be
b
regulated at several points
in the transcription and
translation processes
processes.
E.g., expression of genes
must be precisely
regulated during
development.

Figure 16.13 Potential Points for the Regulation of Gene Expression (Part 2)

(a) Transcriptional control


Eukaryote
y
genes
g
are not organized
g
into operons.
p
Regulation of several genes at once requires
common control elements.
M t eukaryotic
Most
k
ti genes have
h
sequences th
thatt
regulate rate of transcription.
Initiation
t at o o
of ttranscription
a sc pt o involves
o es many
a yp
proteins
ote s ((in
contrast to prokaryotes in which RNA
polymerase directly recognized the promoter).
In eukaryotes there is more complexity than in
prokaryotes and for example the polymerase
requires additional transcription factors to bind to
the DNA

The double helix is stable. So how does RNA polymerase


complex access the single strands?

Transcription factors such as this TATA box binding protein


(TBP) bind promoter sequences. In this case, TBP binds to
the minor groove the TATAAA sequence about 20 nucleotides
( 20 position)
(-20
i i ) upstream off the
h transcription
i i iinitiation
i i i position
ii

Figure 16.14 The Initiation of Transcription in Eukaryotes (Part 1)

In eukaryotes,
transcription factors
(regulatory proteins)
must assemble on the
chromosome before
RNA polymerase can
bind to the promoter.
TFIID binds to the TATA
box; then other
t
transcription
i ti ffactors
t
bind, forming a
transcription complex.

Figure 16.14 The Initiation of Transcription in Eukaryotes (Part 2)

RNA polymerase
II one of the
polymerases in
eukaryotes

B, E, F, H =
other
transcription
factors, which
will
ill be
b different
diff
t
for different sets
of genes/cellular
purposes

Some sequences are common to promoters


of many genes; recognized by
transcription factors in all cells
cells.
Some sequences are specific to a few
genes and are recognized by transcription
factors found only in certain tissues. These
play an important role in differentiation.
differentiation

Figure 16.15 Transcription Factors, Repressors, and Activators

Regulator sequences are located upstream of the promoter.


Regulator proteins bind to these sequences.
sequences Resulting
complex binds to the transcription complex to activate
transcription.

Figure 16.15 Transcription Factors, Repressors, and Activators (Part 2)

Enhancer sequences are farther awayup to 20,000 bp.


Activator proteins bind to enhancer sequences, which
stimulates transcription complex.
Also - negative
g
regulatory
g
y sequences
q
or silencer
sequences turn off transcription by binding repressor
proteins.

16.16 ProteinDNA Interactions

Helix-turn-helix

Zinc finger

Leucine
zipper

Helix-loop-helix

Bases in DNA can form hydrogen bonds


with proteins, especially in major and
minor grooves
grooves.
Many repressor proteins have helix-turnhelix configurationbinding
configuration binding of repressor
prevents other proteins from binding and
initiating transcription
transcription.

Figure 16.17 Coordinating Gene Expression

Regulation of genes that


are far apart or on
different
chromosomes
genes must have
same regulator
g
sequences.

SRE = stress response


element (in plants)

I was walking along the road


with two friends
The sun was setting suddenly
The sky turned blood red
I paused,
d feeling
f li exhausted,
h
d
and leaned on the fence
There was blood and tongues
of fire above the blue-black
blue black
fjord and the city
My friends walked on, and I
stood there trembling with
anxiety
And I sensed an infinite scream
passing
p
g through
g nature.
E. Munch

Edvard Munch, The Scream, 1893

Mental Health
20% of Canadians will
personally experience a
mental illness in their
lifetime.
Suicide accounts for
24% of all deaths among
15-24 year olds and 16%
among 25-44
25 44 year olds
olds.
10-20% of Canadian
youth are affected by a
mental illness or disorder
CMHA, 2013

NATURE, Vol 455,16 October 2008

Figure 16.13 Potential Points for the Regulation of Gene Expression (Part 1)

(b) Chromatin remodeling


Transcription can also be regulated by
changes in chromatin and chromosomes
chromosomes.
DNA is condensed and needs to be
remodeled
d l db
before
f
ttranscription
i ti can occur
Remodeling is facilitated by appropriate
chemical modifications to histone proteins

Figure 16.19 Epigenetic Remodeling of Chromatin for Transcription

Chromatin remodeling:
DNA is wound around
histones to form
n cleosomes which
nucleosomes,
hich
block initiation and
elongation.
One remodeling protein
disaggregates the
nucleosome to allow
initiation (making
space for the
polymerase
complex).
The second remodeling
protein
p
ote b
binds
ds to tthe
e
nucleosomes to allow
elongation to
proceed.

Histone acetylation

Histone p
proteins have tails with p
positively
y charged
g amino
acidsenzymes add acetyl groups:
This reduces positive charges, and decreases affinity of
histones for negatively charged DNA.
Allows chromatin remodeling

Histone modifications

Gene activation requires histone acetyl transferases to add


acetyl groups
groups.
Gene repression requires histone deacetylases to remove
the acetyl groups.
There is more than one type
t pe of chemical modification
The histone codehistone modifications affect gene
activation and repression.
E
Example:
l Methylation
M th l ti off histones
hi t
i associated
is
i t d with
ith
gene inactivation.
Whether a gene becomes activated by chromatin
remodeling
d li may b
be d
determined
t
i db
by histone
hi t
modification [determines whether gene will be
transcribed or not]
Epigenetics: changes in expression that occur without
changing DNA sequence can be stable and heritable in
some circumstances and reversible in others; relevant to
development [and effects of environment on behaviour??
e.g., environment alters methylation patterns of twins
living apart; same pattern at age 3 but different pattern at
50]

Figure 16.18 DNA Methylation: an Epigenetic Change (Part 1)

Not a histone
modification

DNA methylase
catalyses
y addition
of methyl groups to
C at CG (CpG)
sites; represses
transcription need
to remove
(demethylase) to
enable transcription

Epigenetic regulation in
depression (in rats/mice)

BDNF expression
is reduced in the
hippocampus
after social
defeat

e.g., in rat pups


born to mothers
with low levels of
maternal
behaviour (may
be reversible)

BDNF = brain derived neurotophic factor.


factor
BDNF hypothesis of depression (e.g., stress modulates BDNF
signaling)
NATURE|Vol 455|16 October 2008

Figure 16.13 Potential Points for the Regulation of Gene Expression (Part 2)

Figure 14.21 Alternative Splicing Results in Different Mature mRNAs and Proteins

Figure 16.13 Potential Points for the Regulation of Gene Expression (Part 3)

16.5 How Is Eukaryotic Gene Expression Regulated After Transcription?

(d) mRNA stability control


RNA has no repair mechanisms.
mRNA can be catabolized by ribonucleases in the
cytoplasm and lysosomes.
mRNAs have different stabilitiesa mechanism for
posttranscriptional regulation.
Specific AU rich sequences on mRNA [in 3 UTR] can mark
them for breakdown by a ribonuclease complex called an
exosome.
e.g., signaling molecules such as growth factor are only
synthesized when needed and break down rapidly. Their
p
AU sequence
q
and are unstable
mRNAs have a specific

14.5 How Is Eukaryotic Gene Expression Regulated After Transcription?

Micro RNAs (about 20 bases long) bind to


mRNA before it reaches a ribosome.
Causes the mRNA to break down, or inhibits
translation.
The micro RNAs start as a 70 base-pair double
strand.
A protein complex called dicer cuts the RNA
strand.
Small RNAs (siRNA) are under development as
drugs to block gene expression of certain
genes in human diseases
diseases. [2006 Nobel prize]

Figure 16.23 mRNA Inhibition by MicroRNAs

Micro RNAs
Mi
RNA (about
( b t 20
bases long) bind to
mRNA before it
reaches a ribosome.
ribosome
Causes the target mRNA
to break down, or
inhibits translation
translation.
A protein complex called
dicer cuts the parent
RNA strand
strand.
Small RNAs (siRNA) are
under development as
drugs to block gene
expression of certain
genes in human
diseases. [2006 Nobel
prize]
i ]

Figure 16.13 Potential Points for the Regulation of Gene Expression (Part 3)

16.5 How Is Eukaryotic Gene Expression Regulated After Transcription?

(e) Translation control


Little relationship between amount of mRNA and
amount of protein
p
Translational control can keep a balance in the
amount of subunits of proteins.
Example: Hemoglobin has four globin and four
heme units.
If there are more heme than globin units
units, heme
increases rate of translation of globin by
removing
g a block to initiation of translation at
ribosome.

Figure 16.24 A Proteasome Breaks Down Proteins

A protein can be regulated by controlling its lifetime in the cell.


In many cases, an enzyme attaches a protein called ubiquitin to a lysine in a
protein targeted for breakdown.
breakdown
Other ubiquitin chains attach to the first one, forming a polyubiquitin complex.
The whole complex then binds to a proteasome.
Ubiquitin is cut off for recycling; the protein passes by three proteases that digest
it.
it

16.5 How Is Eukaryotic Gene Expression Regulated After Transcription?

Concentrations of many proteins are


determined by their degradation in
proteasomes.
proteasomes
Cyclins are degraded at the correct time in
the cell cycle.
cycle
Transcriptional regulators are broken down
after
ft use; to
t preventt gene to
t be
b always
l
on.

Chapter summary

How Is Eukaryotic
y
Gene Transcription
p
Regulated?
g

Eukaryotic gene expression is regulated both during and after transcription. Review Figure 16.13, WEB
ACTIVITY 16.1

Transcription factors and other proteins bind to DNA and affect the rate of initiation of transcription at the
promoter. Review Figure 16.14 and Figure 16.15, ANIMATED TUTORIAL 16.3

The interactions of these proteins with DNA are highly specific and depend on protein domains and DNA
sequences.

Genes at distant locations from one another can be coordinately regulated by common transcription factors and
promoter elements. Review Figure 16.17
How Do Epigenetic Changes Regulate Gene Expression?

Epigenetics refers to changes in gene expression that do not involve changes in DNA sequences
sequences.

Methylation of cytosine residues generally inhibits transcription. Review Figure 16.18

Modifications of histone proteins in nucleosomes make transcription either easier or more difficult. Review
Figure 16.19

Epigenetic changes can occur because of the environment.

DNA methylation can explain genome imprinting, where the expression of a gene depends on its parental origin.
Review Figure 16.20
How Is Eukaryotic Gene Expression Regulated After Transcription?

Alternative splicing of pre-mRNA can produce different proteins. Review Figure 16.22

MicroRNAs are small RNAs that do not code for proteins, but regulate the translation and longevity of mRNA.
Review Figure 16.23

The proteasome can break down proteins, thus affecting protein longevity. Review Figure 16.24. SEE WEB
ACTIVITY 16.2 for a concept review of this chapter.