Epigenesisand

Development

What is meant by “epigenesis”?

“epi” from Greek meaning “on” or “above”

“genesis” = from Greek, meaning "origin,” “creation” or “generation“

“genetics” = “study of heredity”; a term coined in 1891 by biologist William Bateson

“epigentics,” then, means “above genetics,” or influences in addition to the genome, but mediated via, the genes.

or, more simply put, it refers to genes x environments interactions

Epigenesis (original meaning)

Includes environmentally-induced changes ingene expression

But also includes interactions between the environment and the genome that do not alter gene expression

Defined by phenotype, not genes or environment

Early concepts of epigenesis implied that the fertilized egg contains building materials only, somehow assembled by an unknown directing force.

This contrasted with the then prevalent notion of preformationism, which was a widely held beliefprior to the 1750s.

According to preformationists, a gamete (eitheregg or sperm) contained a perfectly formedembryo that simply grew (became larger)

Current ideas of development are epigenetic inconcept, but far more is now known about whatdirects growth and differentiation.

Inaccurate to speak of a “genetic blueprint”To think of the genome as a blueprint is simply “gene-speak” preformationism

Genes code for proteins

Expression of genes,i.e. which proteins are produced and whenis largely a result of environmental events

induction by surrounding tissuese.g. notochord inducing neural tube

regulation of genes by internal environmente.g. axon guidance

There is no “hard-wired” master control panel directing development.

Sequence of local patterns in which one step in development is a subunit of another

Each step in the developmental hierarchy is a necessary preliminary for the next

Development is four-dimensional

Very early in development, most environmental events controlling gene expression are internal

Later, external environments exert control over gene expression as well

Epigenetics

Second definition used in genetics

Alterations to the DNA, other than changes to the genes themselves (i.e. nucleotide sequence), that:

are passed on with cell divisioncan change normal gene expressioncan be caused by (early) experience

Much more restricted meaning than the first usage

Epigenesis in this second, narrower, mechanistic sense has long been recognized as essential for tissue differentiation and organogenesis

So, what is new?

The environment can also activate or silence genes, leading to different phenotypes,

and that these modifications can be transmitted across generations;i.e. inheritance of acquired characteristicsbut NOT Lamarkian; that is, no change in genome

Epigenomics. 2011 June ; 3(3): 267–277.

Chromatin Structure

Chemical modification of histone proteins in the nucleosome

Nucleosome:DNA wound aroundhistone proteins

Transcriptional Regulation

Histone Modification

Annu. Rev. Psychol. 2010.61:439-466

Transcriptional Regulation

1. DNA Methylation2. Histone Modification3. Transcription Factors

Most well-studied epigenetic mechanism = methylation of cytosine on the DNA

If methylation occurs in an active stretch of DNA, especially a promoter region, gene expression will likely change

Methylation of DNA, and thus gene expression, continues after birth and be influenced by the broader environment

Transcriptional Regulation:DNA Methylation

Methyl group (CH3) added to DNA at CG dinucleotides

Reduces/prevents transcription

Tissue specific

Important in embryogenesis & tissue differentiation

- zygote largely unmethylated

- series of methylations leads to tissue differentiation

Possible source of trans-generational epigenetic transmission

T

G

C

CGCGCGCG

T

T

T

A

A

A

G

A

A

Transcriptional Regulation:DNA Methylation

No methylation:Transcription “stuff” can bind to a promoter

Methylation:Prevents binding to a promoter T

G

C

CGCGCGCG

T

T

T

A

A

A

G

A

A

M

M

M

M

Influences “density” of DNA packaging in chromosomes

Influences transcription

Cocaine & amphetamines (and other drugs) histone modification

Transcriptional Regulation

Histone Modification

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

Alter gene expression without altering DNA itself; i.e. expression is reversibly dependent on presence or absence of transcription factors

Transcriptional Regulation

Transcription Factors

Heritability

What is Heritability?

Heritability is NOT a calculation of, nor is it even an estimate of, the degree to which a phenotypic character is inherited.

Heritability is also NOT a measure of the degree to which a particular character trait is genetic or envronmental.

What is Heritability?

Heritability (H2) IS an estimate ofthe total population variation of a phenotypic character that isattributable to genetic variation.

Thus H2 = Vg/Vt

How is Heritability (H2) Estimated?

Variance of the population (Vt) is partitioned into variance due to genetic variability (Vg), that due to environmental variability (Ve) and their interaction (Vgxe).These sources of variability are assumedto summate, so that: Vt = Vg + Ve +Vgxe

It is not possible to measure Vgxe directly, and is assumed to be negligible.Thus, Vt = Vg + Ve.

It is difficult or impossible to eliminate Ve, whereas Vg is easy to eliminate through the use of inbred strains, clones, or identical twins. Thus, Ve is estimated as the residual variance in genetically homogeneous populations, in which Vg = 0.So, Vt = 0 + Ve.

Since we can easily measure Vt directly and have an estimate of Ve from our genetically homogeneous population, it is a simple matter to calculate Vg in the random population by subtraction:Vg = Vt– Ve

Then H2 = Vg/Vt, and VOILA! we have our heritability estimate.

What assumptions are implicit in this formulation of heritability?

1. that genetic and environmenteffects on phenotypic variability areadditive.2. that gene x environment interactions

are negligible.3. that Ve is the same for inbred and outbred strains.

G Vt = 8Ve = 8Vg = 0H2 = Vg/Vt = 0

Then H2 = Vg/Vt

E

EG Vt = 64

Ve = 8Vg = Vt-Ve = 56H2 = Vg/Vt = 87.5

Vt = 64Vg = 8H2 = Vg/Vt = 12.5

Then H2 = Vg/Vt

G Vt = 8Ve = 0Vg = 8H2 = Vg/Vt = 1

Then H2 = Vg/Vt

E

EG Vt = 64

Ve = 8Vg = Vt-Ve = 56H2 = Vg/Vt = 87.5

Vt = 64Vg = 8H2 = Vg/Vt = 12.5

Then H2 = Vg/Vt

G Vt = 16Ve = 8Vg = 8H2 = Vg/Vt = .5

Then H2 = Vg/Vt

E

EG Vt = 64

Ve = 8Vg = Vt-Ve = 56H2 = Vg/Vt = 87.5

Vt = 64Vg = 8H2 = Vg/Vt = 12.5

Then H2 = Vg/Vt

Heritability quotients depend as much on environmental variation as they do on presumed genetic variation.

Suppose, for example, that one were to estimate the heritability of I.Q., which has been a favorite of many psychologists and educators.

How would selection of sample alter H2?e.g. would you exclude drug-using parents

would your estimate vary according to range of incomes; i.e. would you exclude the very poor who are undernourished or malnourished?

As conceptually flawed as they are, heritability estimates are also limited in that they apply only to the population represented in the sample and cannot be generalized to other populations

Twin Studies

Twin Studies

What independent variables are included?

GeneticMonozygotic vs digyzotic vs siblings vs unrelated

EnvironmentalReared together vs reared apart

Twin Studies

What dependent variable is measured?

ConcordanceAll-or-none, e.g. disease diagnosis.

If one member of the pair has the trait, what is the probabilitythat the other shares that trait?

CorrelationIf a graded trait, e.g. height

Is there a difference in the correlation of the trait in pairsin the different groups?

What are the problemswith twin studies?

i.e., what questionable assumptions are made?

EpigenesisEpigenetic Transmission

Transcriptional Regulation

Pre-translational Regulation

Whole Chromosome Regulation

“interfering” RNA

Methylation

Transcription FactorsHistone Modification

Regulation during Protein Synthesis

“Editing” RegulationAlternative RNA splicing

(X chromosome inactivation or Lyonization)

Regulation after Protein SynthesisMany mechanisms

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:

Alternative RNA Splicing

Polypeptide 1 Polypeptide 2

“Editing” Gene Regulation

Different exons are spliced together to give different polypeptide blueprints

Variation between speciesPossibly why number of human genes is so small

exons are nucleotide sequences that are present in RNA productsintrons are nucleotide sequences that are edited out during RNA splicing

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

RNA InterferenceA short sequence of single-stranded interferingRNA (“iRNA”) and a complex of proteins andenzymes (“silencing stuff”) binds with mRNAand cleaves it.Acts as a “dimmer switch,” reducing translation.

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.

RNA Interference:

Protein Activation/Deactivation

Phosphorylation (add a phosphate group)Acetylation (add an acetyl group)Alkylation (add an ethyl, methyl group)Ubiquitination (adding the protein ubiquitin to an existing protein instructs cellular machinery to degrade/destroy the protein)

Two types of genetic transmissionBlueprint transmission (sequence transmission)

Regulatory transmission (epigenetic transmission)

Transmission of information via the nucleotide sequence (A, C, G, T)

Transmission of information via gene regulationTransmission of genetics above the sequence

of nucleotidese.g., gene methylation and histone modification

Epigenetic Transmission

The expression (active vs inactive) of a gene depends on which parent transmits the gene.

some turned off when inherited from the fatherturned on when inherited from the mother

Others turned on when inherited from fatherturned off when inherited from mother

Mechanismsmethylationphosphorylation of histones

example of epigenetic transmission

Genomic Imprinting

Epigenomics. 2011 June ; 3(3): 267–277.

Epigenomics. 2011 June ; 3(3): 267–277.

Epigenetic Transmission

Behavioral Example: Denenberg & Rosenberg (1967)

Rats either handled or not handled in infancyEarly handling reduces anxiety throughout life

Offspring of handled rats less anxiousOffspring of offspring (“grandchildren”) less anxious

When anxiety is operationally defined as more active in an open field environment

Finally, for the philosophically inclined…Do humans have free will?

Do other animals have free will? I.e., can we make choices or are they illusory products of physiological activity of the brain that we do not adequately understand at present? Are they directed by some greater unknown force or higher power (God)?

If humans have free will, then they can willfully alter their epigenome.

furthermore, willful actions that alter the genome of one generation may then impact future generations; that is, evolution via epigenesis may be driven by free, willful decisions

in humans? in other animals?