Download HGSS2 Epigenesis

Epigenesis:
Synonyms:
Gene Expression, Gene Regulation
Definition:
Anything genetic above and beyond the sequence
of nucleotides
Importance:
Everything, especially development and genetic
responses to the environment.
Examples of Epigenesis:
1) Development: tissue differentiation and timing
1.A) Sex differentiation & behavior
1.B) Chimps versus humans
2) Response to internal and external environment:
2.A) Learning and Memory
2.B) Hormones: Stress and Dominance
“Dimmer Switches” Analogy of Epigenesis
Regulate the amount of active molecules ultimately produced
from DNA blueprints
Active
Molecule
http://www.iconarchive.com/show/medical-icons-by-icons-land/Body-DNA-icon.html
Classification of Epigenesis
I) Epigenetic Transmission
II) Whole Chromosome Regulation
(X chromosome inactivation or Lyonization)
III) Regulation during Protein Synthesis
III.A) Photocopy (Transcriptional) Regulation
III.A.1) Methylation
III.A.2) Histone Modification
III.A.3) Transcription Factors
III.B) “Editing” Regulation
3.B.1) Alternative RNA splicing
III.C) Pre-translational Regulation
3.C.1) “interfering” RNA
IV) Regulation after Protein Synthesis
IV.A) Many mechanisms
I) Epigenetic Transmission
Two types of genetic transmission:
1) Blueprint transmission (sequence transmission)
Transmission of information via
the order of the nucleotides (A, C, G, T)
2) Regulatory transmission (epigenetic transmission)
• Transmission of information about gene regulation
• Transmission of genetics “above and beyond” the
sequence of nucleotides
I) Epigenetic Transmission
• Definitely occurs
• Extent of its importance not known, especially for behavior.
• No empirical evidence, one way or the other, for this in
normal human behavior.
• Mechanisms: methylation, histone modification
I) Epigenetic Transmission
http://discovermagazine.com/2006/nov/cover
I) Epigenetic Transmission
• Behavioral Example: Denenberg & Rosenberg (1967)
(simplified)
• Grandmother rats either handled or not handled at an early age.
• Grandchildren of handled grandmothers were more active (less
anxious) than those of non-handled rats.
I) Epigenetic Transmission:
(Graduate)
Genomic Imprinting: Specific example
of epigenetic transmission
• Definition: The expression (active vs inactive) of a gene depends on
which parent transmits the gene.
• Some genes are turned off when inherited from the father and turned
on when inherited from the mother.
• Other genes are turned on when inherited from father but turned off
when inherited from mother.
• Mechanisms: methylation; phosphorylation of histones.
• No confirmed examples for normal human behavior.
II) Whole Chromosome Regulation:
X Chromosome Inactivation or
Lyonization
• At fertilization, both X chromosomes are active.
• Very soon, however, one of the X chromosomes in a
cell, apparently taken at random, is inactivated and
forms a Barr body.
• All other cells derived from the initial cell have the
SAME X chromosome inactivated.
• Majority of genes on the inactive X chromosome are
not expressed.
II) Lyonization
Barr Bodies =
inactivated X
chromosome
II) Lyonization
(Graduate)
Mechanism
• XIST gene on the X chromosome turns on
and produces XIST RNA.
• Molecules of XIST RNA accumulate along
the chromosome with the active XIST gene.
• The binding of the XIST RNA with the DNA
turns off the genes on that chromosome.
II) Lyonization
Classic Example: Calico Cat
XX
X
X
X
X
Black Fur
X
X
Orange Fur
III) Regulation during protein synthesis
The following slides all illustrate
genetic regulatory mechanisms at
various stages of protein synthesis.
III.A) Transcriptional Regulation:
1. DNA Methylation
2. Histone Modification
3. Transcription Factors
III.A) Transcriptional Regulation:
III.A.1) DNA Methylation
• Methyl group (CH3) added to DNA
• Dimmer switch turned down: Reduces/prevents transcription
• Tissue specific (e.g., genes methylated in the MHC
differ in different tissues)
• Very important in embryogenesis & tissue differentiation
- zygote becomes unmethylated
- series of methylations leads to tissue differentiation
• Possible source of epigenetic transmission
• Human Epigenome Project (map the methylated DNA
areas in the human genome = “methylome”)
III.A) Transcriptional Regulation:
III.A.1) DNA Methylation
Transcription “stuff”
binds and transcribes
CG
G C
CG
G C
CG
G C
CG
GC
T A
A T
T A
T A
A T
G C
T A
A T
CG
A T
A T
G C
(A) Unmethylated
(B) Methylated
Transcription “stuff”
cannot bind
Methyl group
M
M
M
CG
G C
CG
G C
CG
GC
CG
GC
T A
A T
T A
T A
A T
G C
T A
A T
CG
A T
A T
G C
M
M
M
M
M
III.A) Transcriptional Regulation:
III.A.1) Histone Modification
Chemical modification of histone proteins in the
nucleosome
Nucleosome:
DNA (black) wound around
histone proteins (colors)
http://www.scripps.edu/gottesfeld/Sequence-specific.htm
III.A) Transcriptional Regulation:
III.A.1) Histone Modification
• Influences “density” of DNA packaging in
chromosomes
• Influences transcription
• Cocaine & amphetamines (and other
drugs)  histone modification
III.A) Transcriptional Regulation:
III.A.3) Transcription Factors
Transcription factor (regulatory protein)
= protein or protein complex that
enhances or inhibits transcription.
http://www.ncbi.nlm.nih.gov/disease/SRY.html
CREB:
Transcription factor in neurons
CREB
(cyclic AMP Response Element Binding Protein)
Spermatogenesis
CA
cAMP
Circadian
rhythms
Protein
kinases
Drug
Addiction
Long-term
memory
Phosphorylation
Active
CREB
Dopamine
Glutamate Acetylcholine
Serotonin
BDNF
P
CREB
P
CREB
Tyrosine
hydroxylase
P
CREB
BDNF
P
CREB
Glutamate
receptor
1) Various factors initiate 2nd
messenger systems.
2) Second messengers activate
CREB by phosphorylation.
3) Activated CREB acts as a
transcription factor, inducing
the expression of C/EBP genes.
4) C/EBP proteins act as transcription
factors.
http://www.cellscience.com/reviews6/CREB_long-term_memory.html
Enhancer / Repressor
Region, sometimes far away from coding DNA, that
influences gene expression
Enhancer
E
Promoter
DNA
P Coding Region
P Coding Region
E
Enhancers / Repressors
From: http://pbil.univ-lyon1.fr/members/sagot/htdocs/team/projects/chromo_net/purpose_chromo_net.html
HPA Axis:
Example of epigenesis
(hormones & behavior)
CRH
(Hypothalamus)
ACTH
(Pituitary)
-
+
Cortisol
(Adrenal)
Rolling winds send a tree trunk and
debris your way. Thankfully, your stress
system helps you cope. The brain's
hypothalamus releases the hormone
corticotrophin-releasing factor (CRF) and
its effects make your guard go up. CRF
travels to the pituitary gland and triggers
the release of adrenocorticotropic
hormone (ACTH). This hormone travels
in the blood to the adrenal glands and
instructs them to release a third
hormone, cortisol. The hormones rally
the body systems and provide energy to
help you deal with the stressful situation.
You quickly flee. Perpetual or severe
stress, however, may upset the stress
system and harm the brain.
http://web.sfn.org/content/Publications/BrainBriefings/stress.html
http://www.amtamassage.org/journal/su_00_journal/images/body2.jpg
III.B) Editing Gene Regulation
III.B.1) Alternative RNA Splicing
Different exons are spliced together to give
different polypeptide blueprints
RNA transcript before editing:
exon 1
intron 1
exon 1
exon 2
exon 2
exon 3
intron 2
exon 4
mRNA after editing:
Polypeptide Blueprint 1
exon 3
intron 3
exon 4
exon 1
exon 2
intron 4
exon 3
exon 5
exon 5
mRNA after editing:
Polypeptide Blueprint 2
III.B) Editing Gene Regulation
III.B.1) Alternative RNA Splicing
• Varies among species.
• Possible reason why number of human genes is so small.
• Example = Amyloid Precursor Protein (APP) gene.
• Is common in the human brain.
RNA splicing: Tau proteins
DNA:
-1
1
RNA transcript:
-1
1
2
3
4
2
3
4
4a
5
5
6
7
8
7
mRNA variants:
-1
1 2 3 4 5 7 9 10 11 12 13
14
2+, 3+, 10+
-1
1 2 3 4 5 7 9
11 12 13
14
2+, 3+, 10-1
1 2 4 5 7 9 10 11 12 13
14
2+, 3-, 10+
-1
1 2 4 5 7 9
11 12 13
14
2+, 3-, 10-1
1 4 5 7 9 10 11 12 13
14
2-, 3-, 10+
-1
1 4 5 7 9
11 12 13
14
2-, 3-, 10-
9
10
11
12
13
14
9
10
11
12
13
14
III.A.) Pre-translational Epigenesis
III.A.1) RNA Interference:
• Definition: A short sequence of single-stranded
RNA (“iRNA”) and a complex of proteins and
enzymes (“silencing stuff”) binds with mRNA
and cleaves it.
• Result: Decreases the “dimmer switch” by
reducing translation.
• No known human behavioral examples.
• Important method in neuroscience; potential
therapeutic intervention.
See http://www.nature.com/focus/rnai/animations/animation/animation.htm for animated explanation.
III.A.) Pre-translational Epigenesis
III.A.1) RNA Interference:
iRNA =
+
Interfering Stuff =
Forms interfering complex
Binds to mRNA
Cleaves mRNA
mRNA
See http://www.nature.com/focus/rnai/animations/animation/animation.htm for animated explanation.
RNA Interference
(double stranded RNA)
(short interfering RNA)
(RNA-induced silencing complex)
http://www.nature.com/horizon/rna/background/figs/interference_f1.html
Posttranslational Modification:
Protein Activation/Deactivation
• Phosphorylation (add a phoshate group)
• Acetylation (add an acetyl group)
• Alkylation (add a ethyl, methyl group)
• Ubiquitination (add the protein ubiquitin
to an existing protein usually instructs the
cellular machinery to degrade/destroy the
protein)
Epigenesis and
Development
Epigenesis and Development
1.
Zygote (fertilized egg) undergoes massive demethylation
 stem cells
2.
Stem cells become slightly differentiated by various mechanisms
(methylation, histone modification, and transcription factors) but
can still give rise to a number of different tissues.
3.
These cells become further differentiated into tissue cells
(e.g., bone, muscle, neurons, liver cells)
4.
Once a cell becomes fully differentiated in 3, it cannot become
undifferentiated (usually).
Waddington’s Epigenetic Landscape
Zygote
Ectoderm
(outer)
Skin
Neurons
Mesoderm
(middle)
Heart
muscle
Endoderm
(inner)
Skeletal Lung
muscle
Pancreas
Epigenesis and Development
Example: Mammalian Sexual Development
1) Typical Course = Female
2) Males = “Masculinized” Females
2.a) 7th week: SRY gene (sex-determining region
of the Y chromosome) “turns on”
2.b) SRY protein acts as a transcription factor,
influencing the expression of many other
genes
2.c) Mullerian tissue  testes development
2.d) testes produce large amounts of androgens
 masculinization (external genitalia, brain)
http://www.ncbi.nlm.nih.gov/disease/SRY.html
Homeobox Genes
(Graduate)
• Regulate morphology during embryogenesis
• Large family of similar genes
• Often found in clusters
Homeobox Genes: Example
Hox Genes: Regulate axis of development
(Graduate)
Hox Genes: Drosophila and Mus
(Graduate)
http://www.people.virginia.edu/~rjh9u/homeo.html
Hox Genes: Drosophila, Mus & Homo
(Graduate)
http://universe-review.ca/F10-multicell.htm
Hox Genes: Development
(Graduate)
http://universe-review.ca/F10-multicell.htm
Hox Genes, which control the
development of the central nervous
system and the body, are common to
most organisms. Four groups of similar
Hox Genes, shown in color, appear to
control related regions of the human body
and the fly. Each box represents a single
Hox Gene.
http://web.sfn.org/content/Publications/BrainBriefings/hox_genes.html
More examples of
epigenesis
Neurotrophic Factors:
A family of proteins produced in
various tissues that guide the growth,
migration, development and survival of
neurons and repair the processes (e.g.,
dendrites) of damaged neurons
A neuron or support cell (e.g., the
astrocyte) releases the neurotrophic
factor which binds to a receptor. The
binding initiates a signal that regulates
gene transcription. The protein products
then influence the growth, etc. of the
neuron. It may, for example, cause a
process of the neuron to grow in the
direction of the signal.
http://web.sfn.org/content/Publications/BrainBriefings/
neurotrophic.html#fullsize
Axons locate their target tissues by using
chemical attractants (blue) and repellants
(orange) located around or on the surface
of guide cells. Left: An axon begins to
grow toward target tissue. Guide cells 1
and 3 secrete attractants that cause the
axon to grow toward them, while guide
cell 2 secretes a repellant. Surfaces of
guide cells and target tissues also display
attractant molecules (blue) and repellant
molecules (orange). Right: A day later, the
axon has grown around only guide cells 1
and 3.
As the brain develops, neurons
migrate from the inner surface to
form the outer layers. Left:
Immature neurons use fibers from
cells called glia as highways to
carry them to their destinations.
Right: A single neuron, shown
about 2,500 times its actual size,
moves on a glial fiber.
http://web.sfn.org/content/Publications/
BrainBriefings/neuron.html
Experience influences the brain
If bigger brain parts mean a
bigger intellect, musicians may
have a leg up on others. Brain
imaging research shows that
several brain areas are larger in
adult musicians than in
nonmusicians. For example, the
primary motor cortex and the
cerebellum, which are involved in
movement and coordination, are
bigger in adult musicians than in
people who don't play musical
instruments. The area that
connects the two sides of the
brain, the corpus callosum, is also
larger in adult musicians.
http://web.sfn.org/content/Publications/BrainBriefings/music_training_and_brain.htm
Chronic administration of morphine
in rats shrinks dopamine neurons in
the reward circuit. The receiving
branches, called dendrites, wither
and the filaments that transport
important substances down the
neuron's axon are reduced. Nerve
growth factors appear to reverse the
damage.
http://web.sfn.org/content/Publications/BrainBriefings/addiction.html
In the brain, certain cells can release
glutamate. This chemical can then
activate molecular complexes, including
the AMPA receptor and NMDA receptor,
on nearby brain cells and create
reactions that aid memory, according to
studies. Another molecule, the GABA B
receptor, appears to suppress the
process. A number of researchers are
developing and testing compounds that
target components of this system in an
effort to create medicines that can
enhance memory and thinking.
http://web.sfn.org/content/Publications/BrainBriefings/mem_enhance.html
Comparative Genomics
• Tracing similarities/differences in human genes
and genes of other mammals.
• Nascent discipline because genome of our
closest relative (chimp) sequenced in 9/2005.
• Preliminary results suggest that a number of
differences may be due to genes coding for
transcription factors.
• E.g., FOXP2 may influence language; ASPM &
Microcephalin may influence head
circumference.
Anamika et al. (2005)
BMC Genomics, 9:625.
Protein kinase evolution
in humans and chimps.
Green = chimp specific
Black = common
Important question:
How much green
and how much black?