1. Chapter 12. Transcription Activators in Eukaryotes
Ex) p53
DNA-binding domain
Transcription-activation domain
Dimerization domain

2. DNA-Binding Domains I. Zinc-Containing Modules (motif) a. Zinc fingers
b. Zinc modules
c. Modules containing 2 zinc and 6 cysteines
II. Homeodomains ; 60 aa
III. bZIP & bHLH ; leucine zipper

3. Transcription-Activating Domains
- Acidic domains such as yeast GAL4 with 11 acidic amino acids out of 49 amino acids in the domain
- Glutamine-rich domains include Sp1 having 2 that are 25% glutamine
- Proline-rich domains such as CTF which has a domain of 84 amino acids, 19 proline

4. a. Zinc Fingers CxxC-- 12 aa – HxxH (C2H2) Coordination of Zn,
TFIIIA
CxxC-- 12 aa – HxxH (C2H2)
Coordination of Zn,
1 zinc ion per repeat
9 repeats of 30 aa
major groove

5. Arrangement of Three Zinc Fingers in a Curved Shape
The zinc finger is composed of:
An antiparallel β-strand contains the 2 cysteines
2 histidines in an a-helix
Helix and strand are coordinated to a zinc ion

6. b. Zn Module : The GAL4 Protein
a member of the zinc-containing family
It does not have a zinc finger
6 cysteines that coordinate 2 zinc ions (C6)
Dimerization motif with an a-helix that forms a parallel coiled coil

7. c. Modules containing 2 zinc and 6 cysteines (C6):
Nuclear receptors : - Type I ; Steroid hormone receptors ex) Glucocorticoid Receptors
Type II; nucleus
Ex) thyroid hormone R.
Type III; orphan R.
Hsp90
DNA-binding domain with 2 zinc-containing modules

8. III. bZIP & bHLH II. Homeodomains about 60 amino acids
Originally identified in homeobox proteins regulating fruit fly
helix-turn-helix motifs
major groove
A number of transcription factors have a highly basic DNA-binding motif linked to protein dimerization motifs
Leucine zippers
Helix-loop-helix
Examples include:
CCAAT/enhancer-binding protein
MyoD protein
antennapedia
ultrabithorax

9. Four Hypotheses of Enhancer Action
Change in topology
Sliding
Looping
Facilitated tracking
Complex Enhancers (sea urchin Endo16)
Tissue specificity (sea urchin Endo16)

10. Enhanceosome
An enhanceosome is a complex of enhancer DNA with activators contacting this DNA
An example is the HMG that helps to bend DNA so that it may interact with other proteins

11. Insulators Insulators act by:
Enhancer-blocking activity: insulator between promoter and enhancer prevents the promoter from being activated
Barrier activity: insulator between promoter and condensed, repressive chromatin prevents promoter from being repressed

12. Mechanism of Insulator Activity
Sliding model
Activator bound to an enhancer and stimulator slides along DNA from enhancer to promoter
Looping model
Two insulators flank an enhancer, when bound they interact with each other isolating enhancer

13. Phosphorylation and Activation
Activation of a Nuclear Receptor-Activated Gene
Ubiquitylation and Activation