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

2. Same genes, different phenotypes
How?
NOVA’s
A Tale of Two Mice: Chapter 1

3. 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)

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

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

6. 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!
Carey page 90 quote

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

8. NOVA’s Ghost in Your Genes (2006)
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)

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

10. 2. DNA methylation
The addition of methyl groups to DNA, mostly at CpG sites, to convert cytosine to 5-methylcytosine. 5’ 3’
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 3’ 5’
represent potentially heritable changes to the genome

11. DNA methylation is preserved during DNA replication
Stable epigenetic modification; enables differentiated cells to stay differentiated

12. DNA methylation leads to gene silencing
Target gene expressed in normal cell
Normal State
RNA pol TF
Target gene
expressed
Promoter
Target gene inactivated by DNA methylation
Epigenetic Modification TF X
Target gene
not expressed
Promoter
DNA methylation at promoter regions can impede target gene expression
CpG sites are regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence of bases along its length.
*"CpG" stands for cytosine and guanine separated by a phosphate (—C—phosphate—G—), which links the two nucleosides together in DNA.

13. 1) Changes to DNA Methylation leads to gene silencing
Target gene expressed in normal cell
e.g., tumor suppresor gene
Normal State
RNA pol TF
Target gene
expressed
Promoter
Target gene inactivated by hypermethylation
Disease State arising from Epigenetic Modification TF X
Target gene
not expressed
Promoter
DNA methylation at promoter regions can impede target gene expression
CpG sites are regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence of bases along its length.
*"CpG" stands for cytosine and guanine separated by a phosphate (—C—phosphate—G—), which links the two nucleosides together in DNA.

14. 2) Changes to DNA Methylation leads to gene activation
Target gene silenced by methylation
e.g., oncogene
Normal State TF X
Target gene
not expressed
Promoter
Target gene activated by hypomethylation
or demethylation
Disease State arising from Epigenetic Modification
RNA pol TF
Target gene
expressed
Promoter
DNA methylation at promoter regions can impede target gene expression
CpG sites are regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence of bases along its length.
*"CpG" stands for cytosine and guanine separated by a phosphate (—C—phosphate—G—), which links the two nucleosides together in DNA.

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

16. 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.

17. ? 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 ?

18. Genetically Identical Siblings Epigenetic Variation
From the following article:
Environmental epigenomics and disease susceptibility
Randy L. Jirtle and Michael K. Skinner
Nature Reviews Genetics 8, (April 2007)
Environmental epigenomics and disease susceptibility
Randy L. Jirtle and Michael K. Skinner
Nature Reviews Genetics 8, (April 2007)

19. Michael Skinner, A New Kind of Inheritance (2014)
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)

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

21. 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.
TIME MAGAZINE, PERSON OF THE YEAR 2007

22. 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.

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

24. 23% 50% From the following article:
Environmental epigenomics and disease susceptibility
Randy L. Jirtle and Michael K. Skinner
Nature Reviews Genetics 8, (April 2007)
Environmental epigenomics and disease susceptibility
Randy L. Jirtle and Michael K. Skinner
Nature Reviews Genetics 8, (April 2007)

25. Experimental results

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

28. 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.

29. Michael Skinner, A New Kind of Inheritance (2014)
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)

31. 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

32. Inheritance of Epigenetic modifications
Multigenerational
Inheritance from parent to progeny
Meiotic or transgenerational Inheritance by F3 offspring (rare; not documented in human studies to date)
Vinclozolin exposure and rats

33. Rule out the possibility of genetic changes; and,
To demonstrate transgenerational epigenetic inheritance researchers must:
Rule out the possibility of genetic changes; and,
Show that the epigenetic effect can pass through enough generations (F3 or great grandchild) to rule out the possibility of direct exposure.
Genetic Science Learning Center, University of Utah

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

35. If time permits…

36. 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.

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

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

39. 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)

40. Imprinting: an inheritance process independent of Mendelian inheritance

41. Why Imprint? The Genetic Conflict Hypothesis
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
Pg 131 Carey

42. Acetylation is the most highly studied
Histone modifications are more plastic than DNA methylation,

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

44. 1. Histone modification
If the way that DNA is wrapped around the histones changes, gene expression can change.
Histone
Modification
Plastic; enables cell to respond to stimuli, allows for fine tuning of gene expression.

45. Post-translational histone modifications
Although histone modifications occur throughout the entire sequence, the unstructured N-termini of histones (called histone tails) are particularly highly modified. Carey: more than 50 different epigenetic modifications to histones have been identified (2012) – pattern of modifications is called a histone code.