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

2) Response to internal and external environment:

1.A) Sex differentiation & behavior

2.A) Learning and Memory

2.B) Hormones: Stress and Dominance

1.B) Chimps versus humans

Classification of Epigenesis

I) Epigenetic Transmission

III.A) Photocopy (Transcriptional) Regulation

III.C) Pre-translational Regulation

II) Whole Chromosome Regulation

3.C.1) “interfering” RNA

III.A.1) Methylation

III.A.3) Transcription Factors

III.A.2) Histone Modification

III) Regulation during Protein Synthesis

III.B) “Editing” Regulation

3.B.1) Alternative RNA splicing

(X chromosome inactivation or Lyonization)

IV) Regulation after Protein SynthesisIV.A) Many mechanisms

Two types of genetic transmission:1) Blueprint transmission (sequence transmission)

2) Regulatory transmission (epigenetic transmission)

Transmission of information via the order of the nucleotides (A, C, G, T)

• Transmission of information about gene regulation• Transmission of genetics “above and beyond” the

sequence of nucleotides

I) Epigenetic Transmission

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.

• 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.

Genomic Imprinting: Specific exampleof epigenetic transmission

I) Epigenetic Transmission:

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.

Barr Bodies = inactivated Xchromosome

II) Lyonization

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

X

XX

BlackFur

X

X X

OrangeFur

X X

II) Lyonization

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”)

T

G

C

CGCGCGCG

T

T

T

A

A

A

G

A

A

III.A) Transcriptional Regulation:III.A.1) DNA Methylation

No methylation:Transcription

“stuff” can bind to a promoter

Methylated:Prevents

transcription “stuff” from binding to a

promoter

T

G

C

CGCGCGCG

T

T

T

A

A

A

G

A

A

M

M

M

M

Chemical modification of histone proteins in thenucleosome

Nucleosome:

DNA (black) wound aroundhistone proteins (colors)

Figure from Wikipedia entry for nucleosome

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.1) Histone Modification

Transcription factor (regulatory protein) = protein or protein complex that enhances or inhibits transcription.

III.A) Transcriptional Regulation:III.A.3) Transcription Factors

CA cAMPProtein kinases

Phosphorylation

CREB(cyclic AMP Response Element Binding Protein)

Spermato-genesis

Circadian rhythms

Long-term memory

CREB:Transcription factor in neurons

http://www.cellscience.com/reviews6/CREB_long-term_memory.html

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.

Some genes regulated by CREB

CRH

ACTH

Cortisol

+-

(Pituitary)

(Hypothalamus)

(Adrenal)

HPA Axis:Example of hormones & behavior

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

exon 1 intron 1 exon 2 exon 5exon 4exon 3 intron 3intron 2 intron 4RNA transcript before editing:

exon 1 exon 2 exon 4exon 3 exon 1 exon 2 exon 3 exon 5

mRNA after editing: mRNA after editing:

III.B.1) Alternative RNA Splicing

Polypeptide Blueprint 1 Polypeptide Blueprint 2

III.B) Editing Gene Regulation

Different exons are spliced together to givedifferent polypeptide blueprints

• Varies among species.

• Possible reason why number of human genes is so small.

• Examples = Amyloid Precursor Protein (APP) gene, tau proteins

• Is common in the human brain.

III.B.1) Alternative RNA Splicing

III.B) Editing Gene Regulation

RNA splicing: Tau proteins

III.A.) Pre-translational Epigenesis

See http://www.nature.com/focus/rnai/animations/animation/animation.htm for animated explanation.

III.A.1) RNA Interference:

• Definition: A short sequence of single-strandedRNA (“iRNA”) and a complex of proteins andenzymes (“silencing stuff”) binds with mRNAand cleaves it.

• Result: Decreases the “dimmer switch” by reducing translation.

• No known human behavioral examples.

• Important method in neuroscience; potentialtherapeutic intervention.

iRNA = Interfering Stuff = +

Forms interfering complex

mRNA

Binds to mRNA

Cleaves mRNA

See http://www.nature.com/focus/rnai/animations/animation/animation.htm for animated explanation.

III.A.) Pre-translational Epigenesis III.A.1) RNA Interference:

http://www.nature.com/horizon/rna/background/figs/interference_f1.html

(double stranded RNA)

(short interfering RNA)

(RNA-induced silencing complex)

RNA Interference

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 many others) butcan 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 becomeundifferentiated.

The developmental potential and epigenetic states of cells at different stages of development.

Hochedlinger K , Plath K Development 2009;136:509-523NOTE: adapted from Waddington (1957)

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.d) testes produce large amounts of androgens masculinization

Epigenesis and Development

2.c) testes develop

http://www.ncbi.nlm.nih.gov/disease/SRY.html

Homeobox Genes

http://www.people.virginia.edu/~rjh9u/homeo.html

Homeobox & Hox Genes(Drosophila and Mus)

http://universe-review.ca/F10-multicell.htm

Homeobox & Hox Genes(Drossophila, Mus & Homo)

Development(Drosophila and Homo)

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 invarious 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

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

Experience influences the brain

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 evolutionin humans and chimps.

Green = chimp specificBlack = common

Important question:How much greenand how much black?