Section N: Regulation of transcrip. in Euk.Yang Xu, College of Life Sciences Section N Regulation of Transcription in Eukaryotes N1 Eukaryotic Transcription

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


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


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


DNA-binding domainsConsist of:

• Helix-turn-Helix: (a 60aa homeodomain)

• Zinc finger domain: (C2H2 and C4 zinc finger)

• Basic domain: (bZIP or bHLH)


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


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


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.


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


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.


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


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).


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


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


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


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


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)


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


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


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.


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


That’s all for Section N

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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