1. ©2001 Timothy G. Standish James 4:7 7Submit yourselves therefore to God. Resist the devil, and he will flee from you.

2. ©2001 Timothy G. Standish Transcription Regulation Timothy G. Standish, Ph. D.

3. ©2001 Timothy G. Standish Eukaryotic RNA Polymerase II Promoters Eukaryotic promoters comprise several sequence elements spread over about 200 bp upstream from the transcription start site 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. ©2001 Timothy G. Standish Eukaryotic Promoters 5’ 5’ Untrans… Promoter ~200 bp TATA Sequence elements Some sequence elements are also response elements

5. ©2001 Timothy G. Standish 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. ©2001 Timothy G. Standish 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. ©2001 Timothy G. Standish The Heat Shock Response HSTF Hot Cool Kinase Heat shock genes Heat shock response elements

8. ©2001 Timothy G. Standish The Heat Shock Response HSTF Hot Cool Kinase Activation of kinase Phosphorylation of HSTF Heat shock response elements

9. ©2001 Timothy G. Standish Heat shock response elements The Heat Shock Response Hot Cool Kinase Activation of HSTF HSTF Transcription initiation of all heat shock genes with HSEs

10. ©2001 Timothy G. Standish 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 This 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. ©2001 Timothy G. Standish Metallothionein Regulation -260 -240 -220 -200 -180 -160 -140 -120 -100 -80 -60 -40 -20 BLEGC TATA GREMRE TRE MREBLE Basal Level Elements (needed for transcription, act as enhancers) Glucocorticoid Response Element - Behaves as an enhancer and allows regulation by steroids Constitutive Elements Metallothionein Regulator Elements - Multiple copies confer greater levels of induction by heavy metals TGACTCA A consensus sequence to which AP1 binds conferring a response to phorbol esters

12. ©2001 Timothy G. Standish 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. ©2001 Timothy G. Standish 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. ©2001 Timothy G. Standish 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. ©2001 Timothy G. Standish 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. ©2001 Timothy G. Standish Zinc Fingers OH H HO HS H H2NH2N C C C OH H HO N H H2NH2N C C C CH C C NH

17. ©2001 Timothy G. Standish Zinc Fingers Zn ++ H H C C H H C C H H C C ≈ 23 Amino acids 7 - 8 Amino acid linker 2- 4 Amino acids ≈ 6 Amino acids

18. ©2001 Timothy G. Standish