Download Epigenetics 101 - Nationwide Children`s Hospital

Epigenetics 101
Kevin Sweet, MS, CGC
Division of Human Genetics
Learning Objectives
1. Evaluate the genetic code and the role
epigenetic modification plays in common
complex disease
2. Evaluate the effects of vitamin supplementation
in studies of obesity in mice and the process of
DNA methylation
3. Assess how nutrition can have epigenetic effect
on offspring in order to better educate patients
on the impact of nutritional deficiencies
“Genome” refers to the
entire DNA sequence,
and the regulatory
processes
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CATGTACGCATCG
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From Genes to Proteins
2002 Breakthrough: Human Genome
Sequenced
The Genetic Code
A “whole genome” consists of 3 gigabytes
(3 billion “base pairs”) of DNA distributed unequally
amongst 46 chromosomes
~22,000 human genes (2% of the DNA sequence)
Cost for whole genome sequencing has dropped
considerably, esp. in recent years
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The Genetic Code, is not enough
Large scale genomic studies have failed to turn up
variants for common disease
>30 gene variants associated with Type II diabetes;
explains 10% of the disease heritability
Same for heart disease, schizophrenia; HTN
Where is the missing heritability?
80% of the DNA sequence linked to a specific biological
function: ENCODE project; Sept 2012
4 million regulatory regions – turn genes on/off
All disease is complex disease - mix of genetic and nongenetic (environmental, lifestyle) influences
Every cell in the body has all the same genetic
information. Why then do some cells become
brain cells, others cardiac muscle, etc…?
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Epigenetics
Definition
Epigenetics: stable and heritable changes in gene
expression NOT caused by changes in the DNA code
Patterns of gene expression governed by the cellular
material — the epigenome — that sits on top of the
genome, just outside it (hence the prefix epi-, above)
Epigenetics
Term coined in 1942 by Dr. C.H. Waddington:
“The branch of biology which studies the interactions
of genes and their environment that bring the
phenotype into being.” Waddington CH. The Epigenotype. Endeavour 1942; 18–20
It is through epigenetic marks, that our environment
can influence our genes
Relatively new science – both nature and nurture
Epigenetics
DNA code = the notes of an orchestral score
Epigenetics = the Conductor
Epigenetic "marks" tell your genes to switch on or off,
to speak loudly or whisper
It is through epigenetic marks that environmental
factors like diet, stress and prenatal nutrition can
make an imprint on genes, that can then be passed
from one generation to the next
Epigenetics
DNA not freely floating in the cell or nucleus organized with proteins called histones to form a
complex substance: chromatin
Two general states of chromatin:
Euchromatin – open, active genes
Heterochromatin – closed, repressed genes
Epigenetic
Modification
Three main sources (so far)
Histone modification
Autoregulatory
transcription factors –
miRNAs, etc – more
recently described
DNA (cytosine)
methylation – most
extensively studied
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DNA Methylation: Cytosine
DNA Methylation: Cytosine
Methyl marks (CH3) added to cytosine
CpG islands located at the 5’ end of genes, typically contain
promoter and first exons (gene coding regions)
1x108 marks per genome
50-60% of all human genes contain a CpG island
Tissue-specific patterns of CpG island methylation are
established during embryonic development
Change the gene’s expression (turn on/off, dampening
or making it louder – dimmer switch)
Methylated - off or dimmer
Unmethylated - on
DNA Methylation Process Requires
Dietary Methyl Donors and Co-factors
Choline
Betaine
Methionine
Vitamins B6, B12
Folic acid (vitamin B9)
Diet can change DNA methylation patterns
Less methylated
More methylated
The Agouti twin sisters: Genetically identical,
epigenetically different
Waterland & Jirtle 2003 Mol Cell Biol
Supplements: folic acid, B12, choline, betaine
New York Times 7-Oct-03
Waterland & Jirtle 2003 Mol Cell Biol
Methyl Supplementation Changes Coat Color by
Increasing Avy Methylation
Waterland & Jirtle 2003 Mol Cell Biol
Significance of Agouti Mouse Study
Demonstrated causal pathway:
Maternal nutrition – epigenetic change – phenotypic
change
Highlighted the potential role for ‘metastable
epialleles’
Waterland & Jirtle 2003 Mol Cell Biol
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Two Types of Epialleles
Cell type specific epialleles
Different cell types express different genes, controlled in
part by epigenetic mechanisms (nerve cells versus heart
muscle cells)
Metastable epialleles (MEs)
Found in all cell/tissue types
Certain genes which display environmentally responsive
epigenetic marks very early in embryo development
Rare; 40 known genes, i.e. AVY
Is DNA Methylation at Human MEs Affected by Maternal
Nutrition?
Rainy Season - Hungry
(July-November)
Dry Season – Harvest
(December-June)
Seasonal variation in
The Gambia
Rayco-Solon P et al. Am J Clin Nutr 2005;81:134-139
Daily hours of activity in which pregnant rural
Gambian women are active per month
Rayco-Solon P et al. Am J Clin Nutr 2005;81:134-139
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Seasonal Variation in Reproductive Outcomes in
Rural Gambia
Preterm birth
Small for
Gestational
Age
Rayco-Solon P et al. Am J Clin Nutr 2005;81:134-139
Does Season of Conception Affect DNA
Methylation at Metastable Epialleles?
DNA obtained from 3-10 year old children conceived
in West Kiang, Gambia during either:
Rainy (hungry) season (August-September)
Dry (harvest) season (March-May)
Samples matched for year of birth, and sex
Average age: 8 years
1991, 1994, 1995, 1998
N=25 per season
5 MEs examined
Waterland et al 2010 PLoS Genetics
At Five Separate MEs, Methylation was Higher
in Children Conceived in Rainy Season
Waterland et al 2010 PLoS Genetics
At Control Loci, Methylation was Not
Correlated with Season of Conception
Waterland et al 2010 PLoS Genetics
Persistent epigenetic dysregulation and
adult disease
Dutch Hunger Winter (1944-1945)
Individuals peri-conceptually exposed to famine
had less hypomethylation of the imprinted
insulin-like growth factor II (IGF2) gene
(compared to same sex controls)
Key factor in human growth/development
Developmental establishment of DNA methylation
sensitivity to the maternal environment
Children conceived had a 2-fold risk of schizophrenia
Methylation effect still in place, six decades later
Heijmans, T et al Proc Natl Acad Sci 2008 105(44):17046–17049
Fetal basis of adult disease
FETAD hypothesis:
Developmental plasticity and adaptation to
compromised environment and nutritional signals
during early life can program ‘the fetus for a
spectrum of adverse health outcomes as an adult’.
Ex: low birth weight association with increased
risk for adult onset CVD; T2D; depression
Barker et al. J. Intern Med. 2007. 261: 412-417.
DNA Methylation During Mammalian
Development
Perera et al. Reprod Toxicol, 2011 31 (3); 363-373
Expression of imprinted genes in umbilical cord
correlates with growth parameters in human
pregnancy
Many imprinted genes found in clusters
Most share a primary differentially methylated region,
which regulates the genes in a given cluster
Umbilical cord sampling
90 unrelated newborn Chinese babies
Analyzed expression in thirteen imprinted genes
Significant down-regulation of the PEG10 gene in
the LBW babies
Use of specific imprinted genes as new
biomarkers of fetal growth?
Lim et al. J Med Genet 2012;00;1-9.
Dysregulation of imprinted
genes: single gene disorders
Prader-Willi syndrome
Angelman syndrome
Beckwith-Wiederman syndrome
Russell-Silver syndrome
Other neurological syndromes (?)
Certain cancers
Autism (?)
Treatment
Treatments based on epigenetic changes have
not yet been established
Dietary intervention studies have not shown
significant results
Delineate more precisely epigenetic mechanisms
that affect DNA: methylation, histone modification
and microRNAs
Future treatments possible: Altering epigenetic
marks: gene expression, subsequent protein
expression, and phenotype
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Final Thoughts
Can epigenetic changes be permanent? Possibly,
but it's important to remember that epigenetics isn't
evolution. It doesn't change DNA.
Epigenetic changes represent a biological response
to an environmental stressor. That response can be
inherited through many generations via epigenetic
marks, but if you remove the environmental
pressure, the epigenetic marks will eventually fade,
and the DNA code will — over time — begin to revert
to its original programming.
Epigenetic changes will likely provide clues into
various health conditions, particularly common
diseases in the population