Cell Nucleus

Cell Nucleus 

Gene Structure 

Control of Transcription 

1 

Thursday, January 21, 2010

Agenda 

Gene control 

core, proximal and distal promoters 

enhancers 

transcription factors (proteins) 

response elements (DNA code) 

Example: glucocorticoid receptor 

Co-activators 

Mediators of the effect of transcription 

factors. 

Thursday, January 21, 2010 

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- Entire genome in each cell. 

How does cell accomplish 

protein production? How 

does it make sure the correct 

proteins are made, and in 

the right amount? 

3 


Control of Gene Expression in 

Eukaryotes 

Transcription level 

 

if and how often a gene is transcribed. 

Processing level 

 

different messenger RNAs made from a given gene 

(alternative splicing) 

Translational level 

 

How much of the mRNA is made into protein.(and mRNA 

lifetime) 

Post-translation 

 

Protein lifetime 

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Transcriptional Control 

RNA polymerase II transcribes some genes 

much more frequently than others 

This depends on regulatory sites on the 

DNA and the presence of transcription 

factors. 

hnRNA 

“factors” 


5’ 

Regulatory sites 

RNA pol II gene 

3’ 

5

Components of the Promoter 

 

A) Core promoter. DNA sequence, -1 to -40 bases from the 

start of the coding DNA. On/Off regulation of the gene 

regulatory sequence 

TAF 

TBP 

TATA 

core promoter 

RNA polymerase 

RNA start 

gene 

 

It is recognized by a series of DNA-binding proteins: general 

transcription factors, comprising the pre-initiation complex, 

including. 

 

 

TBP (tata binding protein) recognizes the nucleotide sequence 

TATA, about 30 bases back from the start of the gene. 

TAFs (TBP-associated Factors) part of a group of General 

Transcription factors accessory proteins necessary for RNA 

polymerase II 

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B. Proximal promoter (approx. -40 to -150 bases away) 

regulatory sequence 

NF1 

TAF 

TBP RNA polymerase 

gene 

CAAT 

GC 

Proximal promoter 

TATA 

RNA start 

 

 

 

 

CAAT and GC boxes are bound to transcription factors such as NF1 

NF1 recruits a co-activator needed for RNA polymerase to work 

Whereas the core promoter determines whether or not transcription 

can take place, the proximal elements regulate frequency of 

transcription. 

When methylated by the cell, GC regions inactivate the gene 

 

(note, the cell has control, because nothing happens at the core or 

proximal promoter unless all the transcription factors are present) 

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C) Distal promoter. Contains response elements. -500 to -1000 

bases. 

 

Response elements. Special DNA sequence which bind to 

proteins called specific transcription factors 

Transcription factor 

GR 

Response element 

GRE 

500 to 1000 bases 

TATA 


 

 

 

Specific proteins called transcription factors may activate or 

repress transcription activity. Specific to one gene (or a few genes) 

The cell controls gene activity by regulating the presence or 

absence of the specific transcription factor. 

 

 

Eg. Cyclic AMP activates CREB, which binds to its own response 

element and then turns on a gene 

Transcription factors are often activated by dimerization 

Every gene has its own set of response elements. – an integrating 

function. 

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D) Enhancers 

 

 

 

 

 

Specific DNA sequences 

Which bind specific transcription factors, and activate gene expression 

 

Tens of thousands of bases away, but strong 

One enhancer, when activated, activates a number of genes. 

Coordinating function. 

All the genes are usually in one loop, enhancers are separated from other 

loops by insulator proteins. 

Preinitiation complex (one per gene) 

RNA pol 

TATA 

DNA loop, 10,000 bases 

TATA 

RNA pol 

Enhancer 

Transcription factor 

RNA pol 

TATA 

Insulator proteins 


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Example of Transcriptional 

Regulation 

 

 

 

 

 

1. Glucocorticoids released from adrenal gland 

when multicellular animal is injured or ill 

2. enter blood stream 

3. hormone is noticed by responsive cell. 

Receptor/hormone complex is formed in cytoplasm 

4. certain genes are turned on (need a response 

element) 

5. new proteins (PEPCK) are made to do the 

function 

(gluconeogenesis) (provides glucose to cells to 

help them survive the trauma) 

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The Glucocorticoid Receptor 

Glucocorticoid receptor 

protein PEPCK 

translation 

mRNA 

glucocorticoid receptor 

Binds, forms dimer, 

activates NLS 

transcription 

activates gene 

requires correct response element 

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Glucocorticoid receptor: example of 

a specific transcription factor. 

 

Structure 

DNA binding domain, recognizes specific DNA sequence 

Since it is a dimer it recognizes a palindromic sequence 

Activation domain, alters transcription, usually through a corepressor 

or co-activator 

 

 

5’ nnnnnnnnnnnnAGAACAnnnTGTTCTnnnnnn3’ 

3’ nnnnnnnnnnnnTCTTGTnnnACAAGAnnnnnn5’ 

 

Function: how does it turn on the gene? 

Brings in Co-activators which: 

A. Supply general transcription factors for RNA polymerase II, TAFs 

 

B. Alter chromatin structure 

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Response Elements on the PEPCK 

Gene 

PPARγ/RXR 

HNF-3 

Insulin 

GR 

RAR 

T 3 

C/EBP 

Receptor HNF-1 

Fos/Jun 

NF1 

CREB/ 

CREM 

Fos/Jun DBP 

C/EBP 

TBP PolII 

PPARRE 

AF1 GRE 

IRE 

TRE 

P4 P3I 

P3II 

P2 

P1 

TATA 

CRE-1 

PEPCK regulates glucose metabolism 

Regulated by many different hormones 

A site of integration 


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Question: How do 

transcription factors affect 

gene transcription? 


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Question: How do 

transcription factors affect 

gene transcription? 

Answer: 

By altering histone-binding 

and making gene accessible to 

polymerase activity 


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How Transcription Factors 

Work 

Binds to the response elements in the 

Distal promoter region (recognizes the 

nucleotide base sequence) 

Recruits proteins which help the preinitiation 

complex work. These are 

called Coactivators. 

Enhances the RNA polymerase activity 


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More on Coactivators 

Coactivators are proteins which link 

transcription factors, including the 

glucocorticoid receptor to 

general transcription factors needed for 

transcription 

Chromatin re-modeling enzymes 

For the glucocorticoid receptor the 

coactivator protein is called CBP 

coactivator, a type of Histone 

Acetyltransferase (HAT) 

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Histone Acetyltransferase 

acetylates the lysine residues of the 

histones 

this has two effects: 

a) reduces the strength (destabilizes) of the 

histone-DNA interaction; and 

b) reduces interactions between the histone 

proteins 

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Histone Acetyltransferase: 

Step I 

CBP 

H1 

H1 

H1 

H1 

CBP 

TATA 

H1 

H1 

H1 

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Histone Acetyltransferase: 

Step II 

CBP 

RNA 

polymerase 

TAF II 250 

Acetylates 

histones 

TATA 

H1 

Acetylates 

histones 

H1 

H1 

Preinitiation complex has its own histone acetyltransferase activity 

keeps acetylating the histones as it transcribes subunit TAF II 250 


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Transcriptional 

Repression: 

Histone Deacetyltransferases 

DNA Methyltransferases 


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Histone 

Deacetyltransferases 

Histone Deacetylases (HDACs) return 

histones to normal state 

HDAC activity is a property of corepressors 


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DNA Methyltransferases 

Add methyl groups to DNA 

Always at carbon 5 of cytosine 

This essentially ‘tags’ regions of DNA 

so that they are utilized (transcribed) 

differently 

This is a reversible process, but DNA 

methylation is ‘passed-on” ….. 


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“Genomic Imprinting” 

 

 

The state of methylation is passed on to daughter cells: 

 

 

 

Beta-globin genes are less methylated in the fetal liver 

One of the two X-chromosomes is methylated 

Imprinted genes, which are inherited from one parent only, are 

turned off when gametes are made, stay off in the adult 

organism. 

In embryonic development there is a wave of de-methylation 

in first few cell divisions,then re-methylation as cell lineages 

are established.(fig. 12.51, fourth ed.) As the organism 

grows, the cells turn off the genes they –and their progenywon’t 

need in the future. 

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Methylated sites promote gene 

inactivation by de-acetylating 

histones: 

1. Methylated GC islands (in the proximal promoter) 

recruit the binding of the protein MeCP2 

2. MeCP2 in-turn recruits 3. Sin3 co-repressor is a 

histone de-acetylase (HDAC) 

4. which acts by maintaining chromatin condensation, 

inaccessible to RNA polymerase. 

Note, the big question here is how the cell accomplishes the methylation 

in the first place and how it recognizes which genes are to be 

inactivated. Largely still an open question. 

Also note, in this case the DNA itself is methylated. The histones can be 

acetylated, as discussed, and they can be methylated too, which we 

didn’t discuss much. 


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methylated “GC island” 


stops 

H1 

MeCP2 

TATA 

Sin3 

H1 H1 

de-acetylates 

MeCP2 

“recruitment” 

Inactivation of DNA regions by MeCP2/Sin3 

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Main levels of gene 

expression 

1. Genome. (nucleus) Makes gene available for expression 

1. Chromosome de-condensation 

2. DNA methylation 

3. Histone acetylation 

4. Changes in HMG proteins, nuclear matrix 

2. Transcription. Makes primary RNA transcript hnRNA 

1. Control by transcription factors 

3. RNA processing, and nuclear export 

1. RNA splicing, other processing events 

2. Movement into the cytoplasm, where translation happens 

4. Translation (cytoplasm) 

1. mRNA degradation and turnover 

2. Translation control by initiation factors, repressors, microRNAs 

5. Post-translation 

1. Protein folding 

2. Polypeptide cleavage 

3. Modifications 

4. Destination to correct location in the cell, or for secretion 

Resulting Functional protein. 

further regulation by degradation, turnover, phosphorylation etc. 

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Cell Nucleus

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