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Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
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
• 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
Specific trans-factor characteristic
DNA-binding domain activation domain
1. DNA-binding domain
3. Dimerization domain
(in some dimer factor)
2. Activation domain
Transcription factor domain structure
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
DNA-binding domainsConsist 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 domainStructure: 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.
DNA
Helix
Recognition helix
Turn
Helix-turn-helix domain and binding with DNA
3
1
2
3
1
2
Recognition helix
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
Zinc finger domain-I
C2H2 zinc finger:
TFIIIA: 9 repeats; SP1: 3 repeats
C4 zinc finger:
100 steroid hormone transcription factors
Peptide chainDNA binding sites
C
C
C
CZn
H
H H
H
H
R
R
R
Zn
N C
C
C C
C
CC
CCZn Zn
N C
Zinc finger binding with cis-element of DNA
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
Basic domainA 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
Leucine zippers• contain a hydrophobic leucine
residue at every seventh position.
• is often at the C-terminal part of the bZIP protein.
• These leucines are responsible for dimerization through inter-reaction between the -helixes.
• bZIP transcription factors contain Basic domain forms a clam around the DNA.
CLeuLeuLeuLeuLeuLeuLeu
LeuLeuLeuLeuLeuLeuLeu
N N
-helix
Basicdomain
LeuZipper
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
Helix-loop-helixStructure: Hydrophobic (憎
水 ) residues on one side of the C-terminal -helix allow dimerization.
DNA
C
N
C
N
• a nonhelical loop of polypeptide chain separates twoα-helices in each monomeric protein.
• HLH motif is often found adjacent to a basic domain that requires dimerization for DNA binding.
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
Transcription activation domain-IAcidic 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.
b
a
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
Transcription activation domain-IIGlutamine-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
• a continuous run of proline residues can activate transcription;
• For example, in the c-Jun, AP2 and Oct-2 transcription factors
AP2
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
Activation of Tans-factor
(also called acidic domain or acid blobs or negative noodles)
InactivatedTrans-factor
signal
ConformationChanged
Promote transcription
binding DNA
ActivatedTrans-factor
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
N2 Examples of TranscriptionalRegulation
• 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
Generalfactors
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
SP1
TAFII110 TBP
TAFII110 TBP
TFIID
GGGCGG TATA
Housekeeping gene Promoter
+1
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
Hormonal regulation: steroid hormone receptorsSteroid hormones are lipid soluble & can diffuse through cell membranesThe 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 receptorThe 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.
Inhibitor(HSP90)
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
Regulation by phosphorylation:STAT proteinsSignal transduction. This process often involves protein phosphorylation Interferon- induces phosphorylation of a transcription factor called STATIthrough activation of the intracellular kinase called Janus activated kinase.
When STATI protein is unphosphoryl- ated, it exists as a monomer in the cell cytoplasm,when STATI 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.
JAKReceptor
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.
• As a result, the polymerase is able to read through the HIV transcription unit, leading to the productive synthesis of HIV proteins.
• This protein-RNA complex may result in the activation of the kinase activity of TFIIH.
• Tat binds to TAR on one transcript in a complex together with cellular RNA-binding factors.
• This leads to phosphorylation of the CTD of RNA Pol II,
Pol IITrans-Initiation
Complex
Tat Cellularfactor
TFIIHCTDCTD
TAR
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
Cell determination: myoD
Somitescell
Musclecell
Cell determination
myoD gene
myoD protein
P21 waf1/cip1 gene
Fibroblast
CDK
P21 waf1/cip1 Muscle cell
myoD is a transcription factor.
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
Embryonic development: homeodomain proteins
• Homeodomain protein is a TF which was first found in Drosophila
Helix-turn-helix domain and binding with DNA
3
1
23
1
2
• For example, a gene mutation called antennapedia causes legs to grow where antennae would normally be
• Homeotic genes are respon-sible for the correct specification of body parts.
• It is encoded by homeobox, or homeotic gene in Drosophila
Recognition domain
p349 Fig. 12.11
Section N: Regulation of transcrip. in Euk. Yang Xu, College of Life Sciences
That’s all for Section N