unc-chapel hill superfund research program assessing biological responses to contaminants an...

UNC-Chapel Hill Superfund Research ProgramAssessing biological responses to contaminantsAn 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

http://commons.wikimedia.org/wiki/File:Chromosome.gif

Genome vs epigenome

Genome Genes Hardware Static

Epigenome Accessibility to

genes Software Plastic

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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!

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)

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2. DNA methylation The addition of methyl groups to DNA, mostly at

CpG sites, to convert cytosine to 5-methylcytosine.

SAMC 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’

5’

3’

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 cellNormal 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 geneNorm

al 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., oncogeneNorm

al State

Disease State arising from Epigenetic Modification

RNA pol

HOW did these mice become different?

NOVA’s A Tale of Two MiceChapters 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 YellowDominant allele; paternally inheritedAllele is always expressed

a = mutant version of agouti gene

Genetically identical except for agouti gene

Environmental epigenomics and disease susceptibilityRandy L. Jirtle and Michael K. SkinnerNature Reviews Genetics 8, 253-262 (April 2007)http://www.nature.com/nrg/journal/v8/n4/fig_tab/nrg2045_F2.html

GeGenetically 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 susceptibilityRandy L. Jirtle and Michael K. SkinnerNature Reviews Genetics 8, 253-262 (April 2007)http://www.nature.com/nrg/journal/v8/n4/fig_tab/nrg2045_F2.html

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 susceptibilityRandy L. Jirtle and Michael K. SkinnerNature Reviews Genetics 8, 253-262 (April 2007)http://www.nature.com/nrg/journal/v8/n4/fig_tab/nrg2045_F2.html

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 F3

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 (F3 or great grandchild) to rule out the possibility of direct exposure.

Superfund Research ProgramUniversity of North Carolina at Chapel Hillhttp://www.sph.unc.edu/srp/Resources > For educators

Research Translation Core Dana Hainedhaine@unc.edu(919) 843-5735

Contact Information

If time permits…

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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.

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DNA methylation & imprinting Imprinted genes

are inactive due to DNA methylation.

For imprinted genes, only one gene copy is active

http://learn.genetics.utah.edu

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DNA methylation & imprinting Imprinted genes are protected from

reprogramming that occurs in zygote

http://learn.genetics.utah.edu

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

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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

Acetylation is the most highly studied

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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

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1. Histone modification If the way that DNA is wrapped around the

histones changes, gene expression can change.

Histone Modification

http://ehp.niehs.nih.gov/wp-content/uploads/2012/09/WP_Focus_2_Title_web.png

Post-translational histone modifications