11/15/2016

Eukaryotic Models of Gene Regulation Modes of Gene Regulation

Modulation of gene
Gene alteration
expression
Saccharomyces Caenorhabditis Drosophila
elegans
• Gene loss • Transcriptional
• Gene amplification control
• Gene • Post-transcriptional
rearrangement control
• Translational control
Eukaryotes • Post-translational
Gene Regulation Sea urchin Xenopus laevis Arabidopsis control
thaliana

Yeast life cycle Cassette model for mating type switch Cassette model for mating type switch
HMLα MATa HMRa
Chromosome III
HO endonuclease
HMLα HMRa

Gene conversion (frequent)

HMLα MATα HMRa

Gene conversion (frequent)

HMLα MATa HMRa

No change in mating type (rare)

HMLα MATa HMRa

Lewin, Genes VIII

Passarge et al., 2001

Cassette model for mating type switch Cassette model for mating type switch 2. Trypanosome Antigen Variation

Unicellular • African sleeping sickness

• Life cycle alternates in tsetse fly
protozoan and mammal

• Code for variable surface

VSG glycoprotein
genes • Basic copy: telomeric and internal
• Expression-linked copy (ELC)

Lewin, Genes VIII Lewin, Genes VIII

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Activating a VSG gene Activating a VSG gene

Lewin, Genes VIII

3. Generation of Immunoglobulin Diversity The Ig Structure The Ig Structure

Variable (V)

L chain Joining (J)

Gene Ig
Somatic
rearrange-
mutation
ment Diversity kappa Constant
Ig multigene (C)
2 light (L) families
4 polypeptide V, J and C
chains lambda
H chain
2 heavy (H)
Diversity (D)

The Ig Gene Generation of Diversity of the Kappa Light Chain Modes of Gene Regulation
Kappa light chain gene structure
germline DNA J2 J4
V1 V2 V3 V4 C
Modulation of gene
Gene alteration
J3
expression
B-cell DNA
100-300 V 4J C V2 V3 J 2 J 4 C
• Gene loss • Transcriptional
• Gene amplification control
• Post-transcriptional
J3
RNA transcript
V3 J 2 J 4 C
• Gene
rearrangement control
Heavy chain gene structure mRNA • Translational control
V3 J 2 C
• Post-translational
control
protein (kappa light chain)
V C
100-1000 V 10 D 4J C

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Points of control of gene expression Modulation of gene expression A. DNA methylation

Transcriptional Post-transcriptional Translational Post-translational

control control control control
• DNA methylation • RNA processing
• Changes in • RNA turnover
chromatin
• Promoters Methyl 5-
• Enhancers and Cytosine transferases methylcytosine
silencers
• Transcription
factors (general
and gene-
specific)
• Gene control
region

Passarge et al., 2001

B. Changes in the Chromatin C. Promoters Da. Enhancers

Chromatin
Methylation Acetylation Ubiquitylation Phosphorylation remodeling P1 P2 E1 E2 E3 E4 E5

at Lys 9
and 27: Denser:
Activation Activation Activation inactivation
inactivation P1 E1 E2 E3 E4

at Lys 4: Sparser:
activation activation
P2 E2 E3 E4 E5

Passarge et al., 2001

Db. Silencers E. Transcription Factors Gene-specific TF: a. DNA-binding domain

General Gene-specific

http://www.nature.com/
Passarge et al., 2001

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Gene-specific TF: a. DNA-binding domain Gene-specific TF: b. Activation domain c. Dimerization Domain

Passarge et al., 2001

Passarge et al., 2001 http://www.frontiersin.org/

http://www.nature.com/

d. Ligand-binding Domain e. Repressor Domain F. Gene Control Region

http://2011.igem.org/ http://www.nature.com/ Alberts et al.

Regulatory Sequences Eukaryotic Structural Gene

Binding site Spacer
of GRPs sequences
Some Examples of
Adjacent to
promoter
Not bound
by GRPs Transcriptional Regulation in
Far
Eukaryotes
upstream to
promoter
via TFs

Far
downstream
of gene

Within
introns
Passarge et al., 2001

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1. SP1 2. Steroid Hormone Receptor 3. Myogenic Proteins

steroid hormone
1. entry into the cell
inhibitor (HSP90)

glucocorticoid
2. dissociation and receptor
GC-rich Interacts
dimerization
Id
SP1 binding w ith
site TFIIA110

3. nuclear translocation
GRE
GRE = glucocorticoid response element

4. cellular response – induction or suppression of certain genes

eg. estrogen  ovalbumin (storage protein in the eggs of female birds)

4. Gene Regulation in Circadian Clocks 4. Gene Regulation in Circadian Clocks 4. Gene Regulation in Circadian Clocks
Peak at late night to early day

CYTOSOL NUCLEUS CYTOPLASM NUCLEUS CYTOSOL NUCLEUS

Clk Clk
Peak at early night C PPA Peak at early night
Midday to early night k P Late day to early night
P -2
Cyc 2 Cyc
Per DBT Per DBT Per
Tim gene Vri gene
Peak at late evening delayed Peak at early night
Tim P
Tim P P Vri
Tim Midnight Tim Sgg Vri Vri Clk gene
P
Per DBT
Per P
Per DBT Per DBT
P Tim P Clk Pdp1 Pdp1
P P
ε ε
Per gene Pdp1ε gene
Per DBT Cyc Peak at mid to late night
Clk P Clk

Cyc Pdp1 Cyc

Per
ε
a. Transcriptional Feedback: Per/Tim Loop b. Phosphorylation and destabilization of proteins a. Transcriptional Feedback: Clk loop

4. Gene Regulation in Circadian Clocks Post-transcriptional Control Mature eukaryotic mRNA

processing
mRNA
transport
RNA
FP Tim assumption of
rRNA and functional
tRNA
structure

c. Entrainment Passarge et al., 2001

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Examples of Alternative Splicing Post-translational Control

Troponin mRNA: 2
muscle proteins
1. post-translational cleavage
Pituitary Vertebrate Zymogens Procaspases
Ig heavy chains propiomelano- Hedgehog • for digestion • To caspases
differ in –COOH cortin (polyprotein)
• Β-lipotropin
protein • Trypsinogen to • For apoptosis
trypsin
ends (anterior lobe) • self-splicing
• ACTH, α- • Membrane-bound • Chymotrypsinogen
signaling molecule to chymotrypsin
melanotropin and
β-endorphin • Critical for
(intermediate lobe) development
Calcitonin in thyroid
gland vs CGRP in
pituitary gland
Passarge et al., 2001

Post-translational Control Post-translational Control Post-translational Control

4. Formation of tertiary structure
2. Modification of some – proper folding in space
amino acid chains 3. Coupling of molecules to the
protein Alzheimer’s disease
•amyloid protein changes
from α-helical to β-sheet
Acetylation Phosphorylation Hydroxylation conformation
Glycosylation Lipids Coenzymes/cofactors

Formation of S-
Methylation Carboxylation
S linkages

Post-translational Control
5. Quaternary associations of polypeptide
units

pro-insulin  cleavage of C peptide  A + B chains  ACTIVE INSULIN