Epigenetics 101. Kevin Sweet, MS, CGC Division of Human Genetics

Size: px

Start display at page:

Download "Epigenetics 101. Kevin Sweet, MS, CGC Division of Human Genetics"

Beverly Hardy
5 years ago
Views:

1 Epigenetics 101 Kevin Sweet, MS, CGC Division of Human Genetics

2 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

3 Genome refers to the entire DNA sequence, and the regulatory processes GTACATGCGTAGC CATGTACGCATCG 3

4 From Genes to Proteins

5 2002 Breakthrough: Human Genome Sequenced

6 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

7 7

8 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 million regulatory regions turn genes on/off All disease is complex disease-mix of genetic and nongenetic (environmental, lifestyle) influences

9 9 Every cell in the body has all the same genetic information. Why then do some cells become brain cells, others cardiac muscle, etc?

10 Definition Epigenetics Epigenetics: stable and heritable changes in gene expressionnot 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)

11 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; It is through epigenetic marks, that our environment can influence our genes Relatively new science both nature and nurture

12 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

13 Epigenetics DNA not freely floating in the cell or nucleus - organized with proteins called histonesto form a complex substance: chromatin Two general states of chromatin: Euchromatin open, active genes Heterochromatin closed, repressed genes

14 Epigenetic Modification Three main sources (so far) Histone modification Autoregulatory transcription factors mirnas, etc more recently described DNA (cytosine) methylation most extensively studied 14

15 DNA Methylation: Cytosine

16 DNA Methylation: Cytosine Methyl marks (CH 3 ) added to cytosine CpGislands located at the 5 end of genes, typically contain promoter and first exons(gene coding regions) 1x10 8 marks per genome 50-60% of all human genes contain a CpGisland Tissue-specific patterns of CpGisland methylationare 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

17 DNA Methylation Process Requires Dietary Methyl Donors and Co-factors Choline Betaine Methionine Vitamins B6, B12 Folic acid (vitamin B9)

18 Diet can change DNA methylation patterns Less methylated More methylated The Agouti twin sisters: Genetically identical, epigenetically different Waterland & Jirtle 2003 Mol Cell Biol

19 Supplements: folic acid, B12, choline, betaine New York Times 7-Oct-03 Waterland & Jirtle 2003 Mol Cell Biol

20 Methyl Supplementation Changes Coat Color by Increasing A vy Methylation Waterland & Jirtle 2003 Mol Cell Biol

21 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 21

22 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. A VY Is DNA Methylationat Human MEs Affected by Maternal Nutrition?

23 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:

24 Daily hours of activity in which pregnant rural Gambian women are active per month 24 Rayco-Solon P et al. Am J Clin Nutr 2005;81:

25 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:

26 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 Waterlandet al 2010 PLoSGenetics

27 At Five Separate MEs, Methylation was Higher in Children Conceived in Rainy Season Waterlandet al 2010 PLoSGenetics

28 At Control Loci, Methylation was Not Correlated with Season of Conception Waterland et al 2010 PLoS Genetics

29 Persistent epigenetic dysregulation and adult disease Dutch Hunger Winter ( ) 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 (44):

30 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 :

31 DNA Methylation During Mammalian Development Perera et al. Reprod Toxicol, (3);

32 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.

33 Dysregulation of imprinted genes: single gene disorders Prader-Willi syndrome Angelman syndrome Beckwith-Wiederman syndrome Russell-Silver syndrome Other neurological syndromes (?) Certain cancers Autism (?)

34 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 34

35 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

Epigenetic Regulation of Health and Disease Nutritional and environmental effects on epigenetic regulation

Epigenetic Regulation of Health and Disease Nutritional and environmental effects on epigenetic regulation Robert FEIL Director of Research CNRS & University of Montpellier, Montpellier, France. E-mail: