UNC-Chapel Hill Superfund Research Program Assessing biological responses to contaminants An introduction to epigenetics & the exposome

Same genes, different phenotypes How?

Lesson: DNA Wrap-Packaging Matters Learning Objectives  Define the make-up of chromatin  Define epigenetics  Describe DNA methylation as a means of inhibiting transcription  Evaluate impact of environmental agent on gene expression (in mice)

Nucleotide (consists of a base, a 5-carbon sugar, and a phosphate group) Hydrogen Bonds ( between bases) Phosphodiester Bond (between adjacent nucleotides) Decondensed Chromatin Condensed Chromatin

Genome vs epigenome Genome  Genes  Hardware  Static Epigenome  Accessibility to genes  Software  Plastic

What is Epigenetics?  Refers to changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence.  “The study of stable alterations in gene expression potential that arise during development and cell proliferation” (Nature).  Enables a cell/organism to respond to its dynamic external environment during development and throughout life! 6

The Epigenome at a Glance Genetic Science Learning Center, University of Utah

Now it appears that our diets and lifestyles can change the expression of our genes. How? By influencing a network of chemical switches within our cells collectively known as the epigenome. NOVA’s Ghost in Your Genes (2006)

Epigenetic Mechanisms 1.DNA Methylation 2.Histone Modification 3.Small, non-coding RNAs (e.g., micro RNA)

2. DNA methylation  The addition of methyl groups to DNA, mostly at CpG sites, to convert cytosine to 5-methylcytosine. 10 SAM C G T A C A C G A C A C G A T G C A T G T G C T G T G C T A 5’ 3’

DNA methylation is preserved during DNA replication

DNA methylation leads to gene silencing Promoter TF X Target gene not expressed Target gene inactivated by DNA methylation Promoter TF Target gene expressed Target gene expressed in normal cell Normal State Epigenetic Modification RNA pol

1) Changes to DNA Methylation leads to gene silencing Promoter TF X Target gene not expressed Target gene inactivated by hypermethylation Promoter TF Target gene expressed Target gene expressed in normal cell e.g., tumor suppresor gene Normal State Disease State arising from Epigenetic Modification RNA pol

2) Changes to DNA Methylation leads to gene activation Promoter TF X Target gene expressed Target gene activated by hypomethylation or demethylation Promoter TF Target gene not expressed Target gene silenced by methylation e.g., oncogene Normal State Disease State arising from Epigenetic Modification RNA pol

HOW did these mice become different? NOVA’s A Tale of Two Mice Chapters 2 &3

In 2003, a research team at Duke discovered HOW changing the diet of Agouti yellow female mice resulted in genetically identical offspring with altered coat color distribution and disease susceptibility.

Agouti mouse model ? Avy = Agouti Viable Yellow Dominant allele; paternally inherited Allele is always expressed a = mutant version of agouti gene Genetically identical except for agouti gene

Environmental epigenomics and disease susceptibility Randy L. Jirtle and Michael K. Skinner Nature Reviews Genetics 8, (April 2007) Ge Genetically Identical Siblings Epigenetic Variation

The most important effect of epigenetic marks – maybe their reason for existing – might be to wildly expand the number of variant individuals in a population. Michael Skinner, A New Kind of Inheritance (2014)

Environmental epigenomics and disease susceptibility Randy L. Jirtle and Michael K. Skinner Nature Reviews Genetics 8, (April 2007) In this mouse model, a shift in coal color distribution indicates changes in epigenetic modifications.

TIME MAGAZINE, PERSON OF THE YEAR 2007 Dr. Jirtle's pioneering work in epigenetics and genomic imprinting has uncovered a vast territory in which a gene represents less of an inexorable sentence and more of an access point for the environment to modify the genome.

Experiment: Does a maternal diet with soy influence expression of the agouti gene? Female mice were fed genistein, the major phytoestrogen in soy, before and during pregnancy.

Shift in coat color distribution… Genetically identical offspring exhibited varying coat colors.

Environmental epigenomics and disease susceptibility Randy L. Jirtle and Michael K. Skinner Nature Reviews Genetics 8, (April 2007) 50% 23%

Experimental results

Conclusions Read the authors’ conclusions and with a partner discuss how these conclusions could be relevant for humans. Genetic Science Learning Center, University of Utah

Conclusions Our diet, especially during pregnancy, can influence our epigenome and ultimately determine our susceptibility to cancer and disease. Genetic Science Learning Center, University of Utah

But nurture matters too. Many of the contingencies of life- what we eat, what pollutants are in our environment, how often we are stressed – affect how the genes operate. Michael Skinner, A New Kind of Inheritance (2014)

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Epigenetics and fetal development “Epigenetics is being considered an important mechanism through which various stressors can operate. Many lines of evidence point to their being a special concern during rapid fetal development.” Frederica Perera, Columbia Center for Children’s Environmental Health

Inheritance of Epigenetic modifications  Multigenerational Inheritance from parent to progeny  Meiotic or transgenerational Inheritance by F 3 offspring (rare; not documented in human studies to date) Vinclozolin exposure and rats

To demonstrate transgenerational epigenetic inheritance researchers must: Genetic Science Learning Center, University of Utah Rule out the possibility of genetic changes; and, Show that the epigenetic effect can pass through enough generations (F 3 or great grandchild) to rule out the possibility of direct exposure.

Superfund Research Program University of North Carolina at Chapel Hill Resources > For educators Research Translation Core Dana Haine (919) Contact Information

If time permits…

Imprinting  Genomic imprinting is a genetic phenomenon by which certain genes are expressed in a parent-of-origin-specific manner  It is an inheritance process independent of the classical Mendelian inheritance.  The first naturally occurring example of an imprinted gene was the discovery of imprinting in the IGF-2 gene in mice in 1991, and currently about ~150 imprinted genes have been identified in mice and humans. 36

DNA methylation & imprinting  Imprinted genes are inactive due to DNA methylation.  For imprinted genes, only one gene copy is active 37

DNA methylation & imprinting  Imprinted genes are protected from reprogramming that occurs in zygote 38

The Environment & Imprinted Genes  Environmental signals can affect the imprinting process during gamete development  Imprinted genes in the adult are sensitive to environmental signals (since only one gene copy is active)

Imprinting: an inheritance process independent of Mendelian inheritance

Why Imprint? The Genetic Conflict Hypothesis 41 Many imprinted genes are involved in growth and metabolism. Often maternally and paternally imprinted genes work in the very same growth pathways. This conflict of interest sets up an epigenetic battle between the parents -- a sort of parental tug-of-war. Randy L. Jirtle and Jennifer R. Weidman, 2007

Acetylation is the most highly studied 42

3. Non-protein coding RNAs 43  short, non-coding RNAs  e.g., microRNAs  partially complementary to one or more mRNA molecules  post-transcriptional gene regulation, typically down regulation

1. Histone modification  If the way that DNA is wrapped around the histones changes, gene expression can change. 44 Histone Modification

Post-translational histone modifications