Epigenesis and 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 in gene 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 belief prior to the 1750s. According to preformationists, a gamete (either egg or sperm) contained a perfectly formed embryo that simply grew (became larger) Current ideas of development are epigenetic in concept, but far more is now known about what directs 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 when is largely a result of environmental events induction by surrounding tissues e.g. notochord inducing neural tube regulation of genes by internal environment e.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 division can change normal gene expression can 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 characteristics but NOT Lamarkian; that is, no change in genome

Epigenomics June ; 3(3): 267–277.

Chromatin Structure

Chemical modification of histone proteins in the nucleosome Nucleosome: DNA wound around histone proteins Transcriptional Regulation Histone Modification Annu. Rev. Psychol :

Transcriptional Regulation 1.DNA Methylation 2.Histone Modification 3.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 (CH 3 ) 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 C G C G C G C G 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 C G C G C G C G 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 (H 2 ) IS an estimate of the total population variation of a phenotypic character that is attributable to genetic variation. Thus H 2 =V g /V t

How is Heritability (H 2 ) Estimated? Variance of the population (V t ) is partitioned into variance due to genetic variability (V g ), that due to environmental variability (V e ) and their interaction (V g x e ). These sources of variability are assumed to summate, so that: V t = V g + V e +V g x e

It is not possible to measure V gxe directly, and is assumed to be negligible. Thus, V t = V g + V e. It is difficult or impossible to eliminate V e, whereas V g is easy to eliminate through the use of inbred strains, clones, or identical twins. Thus, V e is estimated as the residual variance in genetically homogeneous populations, in which V g = 0. So, V t = 0 + V e.

Since we can easily measure V t directly and have an estimate of V e from our genetically homogeneous population, it is a simple matter to calculate V g in the random population by subtraction: V g = V t – V e Then H 2 = V g /V t, and VOILA! we have our heritability estimate.

What assumptions are implicit in this formulation of heritability? 1.that genetic and environment effects on phenotypic variability are additive. 2.that gene x environment interactions are negligible. 3. that V e is the same for inbred and outbred strains.

G V t = 8 V e = 8 V g = 0 H 2 = V g /V t = 0 Then H 2 =V g /V t E

E G V t = 64 V e = 8 V g = V t -V e = 56 H 2 = V g /V t = 87.5 V t = 64 V g = 8 H 2 = V g /V t = 12.5 Then H 2 =V g /V t

G V t = 8 V e = 0 V g = 8 H 2 = V g /V t = 1 Then H 2 =V g /V t E

E G V t = 64 V e = 8 V g = V t -V e = 56 H 2 = V g /V t = 87.5 V t = 64 V g = 8 H 2 = V g /V t = 12.5 Then H 2 =V g /V t

G V t = 16 V e = 8 V g = 8 H 2 = V g /V t =.5 Then H 2 =V g /V t E

E G V t = 64 V e = 8 V g = V t -V e = 56 H 2 = V g /V t = 87.5 V t = 64 V g = 8 H 2 = V g /V t = 12.5 Then H 2 =V g /V t

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 H 2 ? 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

What independent variables are included? Genetic Monozygotic vs digyzotic vs siblings vs unrelated Environmental Reared together vs reared apart

Twin Studies What dependent variable is measured? Concordance All-or-none, e.g. disease diagnosis. If one member of the pair has the trait, what is the probability that the other shares that trait? Correlation If a graded trait, e.g. height Is there a difference in the correlation of the trait in pairs in the different groups?

What are the problems with twin studies? i.e., what questionable assumptions are made?

Epigenesis Epigenetic Transmission Transcriptional Regulation Pre-translational Regulation Whole Chromosome Regulation “interfering” RNA Methylation Transcription Factors Histone Modification Regulation during Protein Synthesis “Editing” Regulation Alternative RNA splicing (X chromosome inactivation or Lyonization) Regulation after Protein Synthesis Many mechanisms

exon 1intron 1exon 2exon 5exon 4exon 3intron 3intron 2intron 4 RNA transcript before editing: exon 1exon 2exon 4exon 3exon 1exon 2exon 3exon 5 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 species Possibly why number of human genes is so small exons are nucleotide sequences that are present in RNA products introns are nucleotide sequences that are edited out during RNA splicing

See for animated explanation. RNA Interference A short sequence of single-stranded interfering RNA (“iRNA”) and a complex of proteins and enzymes (“silencing stuff”) binds with mRNA and cleaves it. Acts as a “dimmer switch,” reducing translation.

iRNA = Interfering Stuff = + Forms interfering complex mRNA Binds to mRNA Cleaves mRNA See 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 transmission Blueprint transmission (sequence transmission) Regulatory transmission (epigenetic transmission) Transmission of information via the nucleotide sequence (A, C, G, T) Transmission of information via gene regulation Transmission of genetics above the sequence of nucleotides e.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 father turned on when inherited from the mother Others turned on when inherited from father turned off when inherited from mother Mechanisms methylation phosphorylation of histones example of epigenetic transmission Genomic Imprinting

Epigenomics June ; 3(3): 267–277.

Epigenetic Transmission Behavioral Example: Denenberg & Rosenberg (1967) Rats either handled or not handled in infancy Early handling reduces anxiety throughout life Offspring of handled rats less anxious Offspring 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?