Figure 1: Linaria Vulgaris and two different phenotypes of the plant. The two phenotypes have identical genes but different epigenetic states.
Many of us think that phenotype is based specifically off of the genetic code of an organism. This could not be more wrong. Whilst genes influence immensely the phenotype of an organism, we cannot forget that epigenetics, or as I like to call it, "the coding on the coding", also influences silencing and activation of genes in specific cells. The largest modifier of genetic expression is methylation. Methylation is usually associated with silencing of particular genes but can have other effects. Acetylation usually corresponds to activation, but also may have other effects.
http://youngbloodbiology.wikispaces.com/file/view/chromosome1.jpg/111553413/chromosome1.jpg
Figure 2: Molecular biology of the structure of DNA and chromosomes.
As we know, DNA is wrapped around histones, and histone status can affect gene expression. If histones are close together, the position on the DNA where this occurs has reduced expression of the particular genes at that locus. Histones farther apart leaves more room for enzymes to come in and aid in gene expression (and transcription) and vice-versa. The constituents (methylation, acetylation, etc..) on these histones changes their shape slightly and regulates their behavior.
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Figure 3: Acetylation of DNA and histone structure.
When the IAP Avy allele locus, on the mouse genes are methylated, this causes an agouti (or pseudoagouti) coat color. When this is unmethylated, this causes a yellow coat color. Epigenetic information is set up during embryonic development, germ-line development, and also during the first few years of life. Maternal diet and a young child's diet greatly influences the epigenetic state of genes. What causes mottled coat color is methylation of cells during the time when cells are few (a huge ball of cells) and once methylation is set up permanently, this epigenetic markers are mitotically heritable (passed onto each successive daughter cell.
Figure 4: The Avy gene and the resulting phenotype in mice.
Figure 5: Mice with identical genetics, but different epigenetic states, resulting in different phenotype.
This difference in phenotype of while having the same genetic component is termed "variable expressivity" in genetics. It is usually attributed to environment. It is true that environment influences variable expressivity in the phenotype of organisms with the same genes, but we know now that this variable expressivity is due to the difference in epigenetic markers on the genetic code. A good example of a disease with variable expressivity is Waardenburg syndrome. A reason why some carrying a gene like a cancer gene, or disease gene do not show penetrance, is perhaps due to epigenetic markers. That is why not all of those predisposed to disease actually get the disease even when they have the genes for the disease.
Genetic Analysis, Bowman, J., Sanders, M., 2012 Pearson Education Inc Pg. 120.
Figure 6: Pedigree of a family affected by Waardenburg syndrome and the resulting variable expressivity.
Unaccredited pictures taken from DR. Marnie Blewitt, Epigenetic control of gene expression 2014 lecture slides, University of Melbourne.
More reading on epigenetics and disease: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432200/
