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Section N Regulation of
Transcription in Eukaryotes
N1 Eukaryotic Transcription Factors
N2 Examples of Transcriptional
Regulation
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
N1 Eukaryotic Transcription Factors
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Structure of a typical eukaryotic gene
Transcription factor domain structure
DNA-binding domains
Dimerization domains
Transcription activation
Repressor domains
Targets for transcriptional regulation
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Structure of a
typical eukaryotic
gene
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Transcription factor domain structure
Specific trans-factor characteristic
DNA-binding domain
activation domain
3. Dimerization domain
(in some dimer factor)
1. DNA-binding domain
2. Activation domain
DNA-binding domains
Consist of:
• Helix-turn-Helix: (a 60aa homeodomain)
• Zinc finger domain: (C2H2 and C4 zinc finger)
• Basic domain: (bZIP or bHLH)
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Helix-turn-helix domain
Structure: a 60aa homeodomain
encoded by the homeobox.
Found in:
Helix
• Antennapedia TF of Dropphila
• Phage DNA-binding proteins
such as the l cro repressor;
Turn
Recognition
helix
• Lac and trp repressors;
• cAMP receptor protein, CRP.
DNA-binding domain:
• Recognition helix, lies partly in
the major groove and interacts
with the DNA.
Section N: Regulation of transcrip. in Euk.
DNA
Yang Xu, College of Life Sciences
Helix-turn-helix domain and binding with DNA
Recognition helix
2
2
3
3
1
1
Zinc finger domain-I
DNA binding sites
R
C
N
C
Zn
R
H
H
R
H
C H
Zn
C H
Peptide chain
C2H2 zinc finger:
C
TFIIIA: 9 repeats; SP1: 3 repeats
C4 zinc finger:
C
N
C
Zn
C
C
C
C
Zn
100 steroid hormone transcription
factors
C
C
Section N: Regulation of transcrip. in Euk.
C
Yang Xu, College of Life Sciences
Zinc finger binding with cis-element of DNA
Basic domain
A basic domain is found in a number of DNAbinding proteins and is generally associated
with:
• the leucine zipper (ZIP) motif or
• the helix-loop-helix (HLH) motif
These are referred to as:
• basic leucine zipper (bZIP) protein or
• basic helix-loop-helix (bHLH) protein.
Dimerization of the proteins brings together
two basic domains which can then interact
with DNA.
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Leucine zippers
• contain a hydrophobic leucine
residue at every seventh position.
• is often at the C-terminal part of
the bZIP protein.
C
Leu
Zipper
N
Leu
Leu
Leu
Leu
Leu
Leu
Leu
Leu
Leu
Leu
Leu
Leu
Leu
Leu
a-helix
Basic
domain
Section N: Regulation of transcrip. in Euk.
N
• These leucines are responsible
for dimerization through interreaction between the a-helixes.
• bZIP transcription factors contain
Basic domain forms a clam
around the DNA.
Yang Xu, College of Life Sciences
Helix-loop-helix
C
Structure: Hydrophobic (憎水)
residues on one side of the
C-terminal a-helix allow
dimerization.
• a nonhelical loop of
polypeptide chain separates
two α-helices in each
monomeric protein.
• HLH motif is often found
adjacent to a basic domain
that requires dimerization for
DNA binding.
C
N
N
DNA
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Transcription activation domain-I
Acidic activation
domains:
a
• have a very high
proportion of acidic amino
acids;
• Trans-activation domains
of yeast Gal4 (a) and
mammalian glucocorticoid
receptor (b);
• are characteristic of many
transcription activation
domains.
b
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Transcription activation domain-II
Glutamine-rich
domains
• have a very high
proportion of
glutamine amino acids;
• In two activation
regions of the
transcription factor
SP1 (TATA box).
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Transcription activation domain-III
Proline-rich domain
AP2
• a continuous run of proline residues
can activate transcription;
• For example, in the c-Jun, AP2 and
Oct-2 transcription factors
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Transcription activation domain-IV
• Transcription activation domain
have a very high proportion of acidic amino acid
(also called acidic domain or acid blobs or negative noodles)
Activation of Tans-factor
Inactivated
Trans-factor
Conformation
Changed
signal
Activated
Trans-factor
Promote
transcription
binding DNA
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
N2 Examples of Transcriptional
Regulation
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Constitutive transcription factors: SP1
Hormonal regulation: steroid hormone receptors
Regulation by phosphorylation: STAT proteins
Transcription elongation: HIV Tat
Cell determination: myoD
Embryonic development: homeodomain proteins
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Constitutive transcription factors: SP1
SP1 is a very common transcription factor which
contains (SP1 is present in all cell types):
• three zinc finger motifs and
• two glutamine-rich transactivation domains.
TAFII110
SP1
TAFII110
TBP
SP1
GGGCGG TATA
TBP
TFIID
General
factors
+1
Housekeeping gene Promoter
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Hormonal regulation:
steroid hormone receptors
Inhibitor
(HSP90)
Steroid hormones are lipid soluble &
can diffuse through cell membranes
The TF called steroid hormone
receptors.
In the absence of the steroid hormone,
the receptor is bound to an inhibitor,
and located in the cytoplasm.
The steroid hormone binds to the
receptor and releases the receptor
The receptor to dimerize and
translocate to the nucleus.
The DNA-binding domain of the steroid hormone receptor then
interacts with its specific DNA-binding sites.
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Regulation by phosphorylation:
STAT proteins
Signal transduction. This process often
involves protein phosphorylation
Interferon- induces phosphorylation
of a transcription factor called STATIa
through activation of the intracellular
kinase called Janus activated kinase.
Receptor
JAK
When STATIa protein is unphosphorylated, it exists as a monomer in the
cell cytoplasm,
when STATIa becomes phosphorylated
at a specific tyrosine residue, it is able
to form a homodimer
which moves from the cytoplasm into
the nucleus & bind to a DNA-binding.
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences
Transcription elongation: HIV Tat
•
Tat is protein encoded by HIV
• Tat can make mammalian cells in
transcription elongation state.
• Tat binds to an RNA stem-loop
structure called TAR, just after the
HIV transcription start site.
Trans-Initiation
Complex
TFIIH
Pol II
CTD
TAR
• Tat binds to TAR on one transcript
in a complex together with cellular
RNA-binding factors.
• This protein-RNA complex may
result in the activation of the kinase
activity of TFIIH.
• This leads to phosphorylation of the
CTD of RNA Pol II,
Section N: Regulation of transcrip. in Euk.
Cellular
factor
• As a result, the polymerase is able to
read through the HIV transcription
unit, leading to the productive
synthesis of HIV proteins.
Tat
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Cell determination: myoD
myoD is a transcription factor.
Somites
cell
Cell determination
myoD gene
myoD protein
Section N: Regulation of transcrip. in Euk.
Muscle
cell
P21 waf1/cip1 gene
P21 waf1/cip1
CDK
Muscle cell
Fibroblast
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Embryonic development:
homeodomain proteins
• Homeodomain protein is a
TF which was first found
in Drosophila
Helix-turn-helix domain and binding with DNA
3 2
2
3
1
1
• It is encoded by homeobox,
or homeotic gene in Drosophila
Recognition domain
• Homeotic genes are responsible for the correct
specification of body parts.
• For example, a gene mutation
called antennapedia causes
legs to grow where antennae
would normally be
Section N: Regulation of transcrip. in Euk.
p349 Fig. 12.11
Yang Xu, College of Life Sciences
That’s all for Section N
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences