1. Relationship between Genotype and Phenotype
Molecular Basis for
Relationship between Genotype and Phenotype
genotype
DNA
DNA sequence
transcription
RNA
translation
amino acid
sequence
protein
function
phenotype
organism

2. Cis-acting Regulatory Elements
Promoter
- located near transcription-initiation site
- binds RNA polymerase II
Promoter-proximal Elements
- located near promoter
- binds proteins that assist RNA polymerase binding
Distance-independent Elements
- enhancers: increase transcription rates
- silencers: decrease transcription rates

3. Promoter and Promoter-proximal Elements
In all cells, constitutive expression of transcription factors that bind to upstream promoter elements ensures active transcription at all times.

4. Promoter and Promoter-proximal Elements
Effect of point mutations on transcription rate of b-globin gene.
In general, transcription rate is reduced when base sequence is changed in the core promoter and promoter-proximal elements.

5. Distance-independent Cis-acting Elements
Both enhancers and silencers affect transcription rate. Each has unique DNA sequence for the binding of regulatory proteins.
Enhancer sequences contain multiple binding sites for trans-acting regulatory proteins.
Enhancers could be located upstream from the promoter, downstream from the gene, or even within an intron of a gene.

6. Distance-independent Cis-acting Elements
Interaction between regulatory proteins that bind to enhancer elements and promoter-proximal elements with RNA polymerase initiates transcription at appropriate levels.
Architectural proteins allow bending of the DNA to bring all components together, both spatially and functionally.

7. Regulatory Proteins that Modulate Transcription
These proteins contain one or more functional domains:
Recognize DNA regulatory sequence
Interact with transcriptional apparatus proteins (RNA polymerase, proteins associated with RNA polymerase)
Interact cooperatively with other regulatory proteins bound to DNA sequence
Influence chromatin condensation
Act as sensor of intracellular physiological conditions

8. Transcription Factors
Transcription factors have:
DNA binding domain (interact with promoter-proximal elements or enhancers/silencers)
Transactivation domain (activate or repress transcription, involved in protein/protein interaction)

9. Structural Families of Transcription Factors and Regulatory Proteins:
Helix-Turn-Helix:
Zinc-Finger:
Leucine Zipper:
Helix-Loop-Helix:
Many homeotic genes code for TF's of this class.
Many steroid hormone receptor protein TF's belong to this class.
Proto-oncogenes such as c-jun and c-fos are genes that encode TF's of this class.
Certain proto-oncogenes and genes involved in differentiation encode TF's of this class.

10. Structural Families of Transcription Factors and Regulatory Proteins:
Zinc-Finger: Leucine Zipper:
Helix-Loop-Helix:

11. Tissue-specific Regulation of Transcription
Regulated transcription depends on:
- specific enhancer for gene(s)
- enhancer-specific activator proteins
- correct interaction between enhancer and activator
Tissue-specific regulation requires that the enhancer-specific activator is present only in cells of that tissue type.
ectopic expression: expression in an abnormal location

12. “Master Switch” Gene
Eye formation requires over 2000 genes.
eyeless (ey) mutation causes small rudimentary eyes to form in Drosophila melanogaster.
Small eyes (Sey, Pax-6) in mouse causes similar phenotype.
Aniridia gene in human (lack of normal iris) shows considerable homology to ey gene.

13. Comparison of ey+ and ey Phenotypes
Wild-type eyes
eyeless (ey) eyes
size of ey eyes

14. eyeless (ey) gene codes for a helix-turn-helix transcription protein.
“Master Switch” Gene
Wild-type eyeless (ey) gene can be induced to be expressed ectopically.
eyeless (ey) gene codes for a helix-turn-helix transcription protein.