1. 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

2. N1 Eukaryotic Transcription Factors
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

3. Structure of a typical eukaryotic gene
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

4. 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

5. 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

6. Helix-turn-helix domain
Structure: a 60aa homeodomain encoded by the homeobox.
Found in:
Antennapedia TF of Dropphila
Phage DNA-binding proteins such as the l cro repressor;
Lac and trp repressors;
cAMP receptor protein, CRP.
DNA-binding domain:
Recognition helix, lies partly in the major groove and interacts with the DNA.
Helix
Recognition
helix
Turn
DNA
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

7. Helix-turn-helix domain and binding with DNA3 1 2
Recognition helix

8. Zinc finger domain-I Peptide chain R C C2H2 zinc finger:
DNA binding sites
Peptide chain C Zn H R N
C2H2 zinc finger:
TFIIIA: 9 repeats; SP1: 3 repeats
C4 zinc finger:
100 steroid hormone transcription factors C Zn N
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

9. Zinc finger binding with cis-element of DNA

10. Basic domain
A basic domain is found in a number of DNA-binding 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

11. Leucine zippers C a-helix Zipper
contain a hydrophobic leucine residue at every seventh position.
is often at the C-terminal part of the bZIP protein. C
Leu N
a-helix
Basic
domain
Zipper
These leucines are responsible for dimerization through inter-reaction between the a-helixes.
bZIP transcription factors contain Basic domain forms a clam around the DNA.
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

12. Helix-loop-helix C N C N
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.
DNA
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

13. Transcription activation domain-I
Acidic activation domains:
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. a b
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

14. 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

15. Transcription activation domain-III
AP2
Proline-rich domain
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

16. Transcription activation domain-IV
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
signal
Conformation
Changed
Promote
transcription
binding DNA
Activated
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

17. N2 Examples of Transcriptional Regulation
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

18. 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.
SP1
TAFII110
TBP
TFIID
General
factors
TAFII110
TBP
SP1
GGGCGG TATA
Housekeeping gene Promoter +1
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

19. 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

20. Regulation by phosphorylation: STAT proteins
Receptor
Signal transduction. This process often involves protein phosphorylation
JAK
Interferon- induces phosphorylation
of a transcription factor called STATIa
through activation of the intracellular
kinase called Janus activated kinase.
When STATIa protein is unphosphoryl-
ated, 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

21. 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.
Pol II
Trans-Initiation
Complex
CTD
CTD
TFIIH
TAR
Tat binds to TAR on one transcript in a complex together with cellular RNA-binding factors.
Tat
Cellular
factor
This protein-RNA complex may result in the activation of the kinase activity of TFIIH.
As a result, the polymerase is able to read through the HIV transcription unit, leading to the productive synthesis of HIV proteins.
This leads to phosphorylation of the CTD of RNA Pol II,
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

22. Cell determination: myoD
myoD is a transcription factor.
Cell determination
Somites
cell
Muscle
cell
myoD gene
P21 waf1/cip1 gene
CDK
myoD protein
P21 waf1/cip1
Muscle cell
Fibroblast
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

23. Embryonic development: homeodomain proteins
Helix-turn-helix domain and binding with DNA 3 1 2
Embryonic development: homeodomain proteins
Homeodomain protein is a TF which was first found in Drosophila
It is encoded by homeobox, or homeotic gene in Drosophila
Recognition domain
Homeotic genes are respon-sible for the correct specification of body parts.
For example, a gene mutation called antennapedia causes legs to grow where antennae would normally be
p349 Fig
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences

24. That’s all for Section N
Section N: Regulation of transcrip. in Euk.
Yang Xu, College of Life Sciences