1. James 4:7
7 Submit yourselves therefore to God. Resist the devil, and he will flee from you.

2. Regulation of Transcription
Timothy G. Standish, Ph. D.

3. Eukaryotic RNA Polymerase II Promoters
Eukaryotic promoters are made up of a number of sequence elements spread over about 200 bp upstream from the transcription start site
In addition to promoters, enhancers also influence the expression of genes
Control of gene expression in eukaryotes involves many more factors than control in prokaryotes
This allows much finer control of gene expression

4. Some sequence elements are also response elements
Eukaryotic Promoters 5’
Exon 1
Promoter
TATA
Sequence elements
~200 bp
Some sequence elements are also response elements

5. Response Elements
Response elements are short sequences found either within about 200 bp of the transcription start site, or as part of enhancers
Different genes have different response elements
Binding of transcription factors to response elements determines which genes will be expressed in any cell type under any set of conditions

6. Heat Shock Response Elements
Sudden changes in the temperature of cells cause stress in response to which heat shock genes are expressed
At least some heat shock genes are thought to be chaperones that help proteins fold correctly
Heat shock genes have Heat Shock Elements (HSEs) in their control regions
Heat Shock Transcription Factors (HSTFs) bind the HSEs up regulating expression of heat shock gene products

7. The Heat Shock Response
Hot
Cool
HSTF
Kinase
Heat shock genes
Heat shock response elements

8. The Heat Shock Response
Hot
Cool
Activation of kinase
HSTF
Kinase
Phosphorylation of HSTF
Heat shock response elements

9. The Heat Shock Response
Activation of HSTF
Kinase
Hot
Cool
HSTF
Transcription initiation of all heat shock genes with HSEs
Heat shock response elements

10. Metallothionein Regulation
Heat shock protein regulation illustrates how a group of genes can be regulated by a single transcription factor
Other genes are regulated by a group of transcription factors which allows them to either respond to multiple separate situations, or respond only to a specific combination of situations
Metallothionein is an example of a gene that can be turned on by multiple transcription factors

11. Metallothionein Regulation
Glucocorticoid Response Element - Behaves as an enhancer and allows regulation by steroids
TGACTCA
A consensus sequence to which AP1 binds conferring a response to phorbol esters
BLE GC
TATA
GRE
MRE
TRE
Basal Level Elements
(needed for transcription, act as enhancers)
Metallothionein Regulator Elements - Multiple copies confer greater levels of induction by heavy metals
Constitutive Elements

12. Regulation By TFs
A single transcription factor (or group of transcription factors) may regulate expression of a group of genes (i.e., heat shock proteins)
A single gene may be regulated by a number of independent transcription factors (i.e., metallothionein)
Eukaryotic regulation does not seem to involve repression
To achieve high levels of expression, several different transcription factors binding to different response elements may be necessary

13. How Do TFs Recognize Response Elements?
Some mechanism must exist for protein transcription factors to recognize the specific sequences of bases found in response elements
There is no known specific relationship between a given amino acid and a base that would allow direct recognition
Groups on bases that are not involved with base pairing have the potential to be recognized by proteins
Some specific sequences are known to influence the gross structure of DNA

14. DNA Binding Domains
Transcription factors exhibit a number of different motifs found in the area known to bind DNA:
Zinc finger -First found in TFIIIA
Helix-turn-helix - First described from phage receptors
Amphipathic Helix-loop-helix - Identified in some development regulators
Leucine zipper - Held together by interactions between leucine amino acids

15. Zinc Fingers
Are found in steroid receptors and are common in other transcription factors
Interaction between cysteine and histidine amino acids and the divalent zinc ion results in the formation of loops called “fingers”
One side of each loop forms an a-helix which can lie in the major grove of DNA
Interaction between the amino acids in the zinc finger and bases in the DNA allow for sequence recognition

16. Zinc Fingers OH H O HS
H2N C OH H O N
H2N C

17. Zinc Fingers Zn++ Zn++ H C ≈ 6 Amino acids H C ≈ 23 Amino acids 2- 4
7 - 8 Amino acid linker

18. The
End