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Molecular Basis for
Relationship between Genotype and Phenotype
genotype
DNA
DNA sequence
transcription
RNA
translation
protein
function
phenotype
organism
amino acid
sequence
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
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.
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.
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.
Distance-independent Cis-acting Elements
Interaction between
regulatory proteins that
bind to enhancer
elements and promoterproximal 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.
Regulatory Proteins that Modulate Transcription
These proteins contain one or more functional domains:
1. Recognize DNA regulatory sequence
2. Interact with transcriptional apparatus proteins (RNA
polymerase, proteins associated with RNA
polymerase)
3. Interact cooperatively with other regulatory proteins
bound to DNA sequence
4. Influence chromatin condensation
5. Act as sensor of intracellular physiological conditions
Transcription Factors
Transcription factors have:
1. DNA binding domain (interact with
promoter-proximal elements or
enhancers/silencers)
2. Transactivation domain (activate or
repress transcription, involved in
protein/protein interaction)
Structural Families of Transcription Factors and Regulatory Proteins:
Helix-Turn-Helix:
Many homeotic genes code for TF's of this
class.
Zinc-Finger:
Many steroid hormone receptor protein TF's
belong to this class.
Leucine Zipper:
Proto-oncogenes such as c-jun and c-fos are
genes that encode TF's of this class.
Helix-Loop-Helix:
Certain proto-oncogenes and genes involved
in differentiation encode TF's of this class.
Structural Families of Transcription Factors and Regulatory Proteins:
Zinc-Finger:
Leucine Zipper:
Helix-Loop-Helix:
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
“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.
Comparison of ey+ and ey Phenotypes
Wild-type eyes
eyeless (ey) eyes
size of ey eyes
“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.