4/20/2016. Objectives. Epigenetic Definitions. Gene Expression. More Questions. Questions to Consider

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1 Objectives Epigentics: You Might Be What Your Grandmother Ate Lynda Britton, Ph.D., MLS(ASCP) CM Professor LSU Health Shreveport Discuss epigenetics and its role in cancer, imprinting and X chromosome inactivation. Describe the modifications/mechanisms of DNA marks that result in epigenetic changes. Discuss the role of epigenetics in environmental exposures. Epigenetic Definitions Gene Expression Heritable genetic modification not in primary DNA sequence Underpin development, regulation and maintenance of normal cells Modified by lifestyle, nutrition and environment Molecular factors/processes around the DNA that regulate genome activity, independent of DNA sequence, and are mitotically stable Questions to Consider Genes make proteins: How are only the right genes expressed in a cell type? How does the genotype produce the phenotype? How are traits inherited without changes in the DNA sequence? More Questions Protein coding DNA sequences are 1% of the genome: What is the rest used for? How does the structural adaptation influence gene activity? Most of the genome is inaccessible: How does the gene activation machinery gain and/or keep access 1

2 More Questions Epigenetic Changes in Twins How are characteristics inherited across the cell or organism generations without changes in the DNA sequence? How are changes influenced by the environment? Is it Nature vs Nurture? Nature vs Nurture Dutch Famine of 1944 Överkalix Study Obesity Diabetes Breast cancer Lung and Kidney Isolated with periodic famine and feast Paternal grandfather s food supply linked to mortality of grandsons Females had 2 x higher mortality if grandmother had much food between ages 8-10 Lower risk of CVD if father s food supply was poor or the mother s was good Obesity Obesity Depression 2

3 Schizophrenia 1% chance in general population 50% chance if homozygous twins Childhood Stress Even if removed from abuse some develop: Depression Self-harm Drug abuse Suicide Epigenetic Programming by Maternal Behavior Mice Study Epigenome Chemical compounds that modify or mark the DNA 3

4 Epigenetic Marks Determine accessibility of transcription machinery Controls gene expression Set during development Most removed during sperm and egg production Some passed on Types of Epigenetic Changes DNA methylation Histone modification Non-coding RNA Chromatin modification Methylation Gene promotor Repetitive DNA elements Transposons Histone Modification Chromatin Nucleosome 150 bp DNA around 8 histone proteins H2A H2B H3 H4 Regulate access to DNA Docking station for interactions Histones in the Nucleosome 4

5 Kabuki Syndrome Rare complex disorder Mental retardation, short stature, facial Mutation in gene that adds methyl groups --histone methyltransferase Regulation by MicroRNA (RNAi)(RNAsi) Small noncoding RNAs are typically only ~18 40 nucleotides in length 1000 are bp target multiple protein coding mrnas Have been shown to play critical roles in cellular processes Developmental timing Cell fate Tumor progression Neurogenesis Micro RNAs and Short Interfering RNAs When egg and sperm meet, zygote must be reprogrammed as blank slate Epigenetic tags removed Small number of genes, tags retained ~1% of genes escape epigenetic reprogramming through a process called Imprinting DNA Imprinting DNA modification main method of genomic imprinting Imprinting gamete specific silencing of genes Maintains balanced expression of genes in growth and embryonic development by selective methylation of homologous genes Occurs in gametogenesis; differs in male and females Genomic Imprinting Gene is methylated to show the parent of origin Only small percentage of genes Cluster on short arm of chromosome 11 and long arm of chromosome 15 5

6 Imprinting Controlled by methylation If copy from the father is methylated, it is switched off If copy from mother is not methylated, it is switched on Promotor region is methylated, not gene Placenta and brain have most imprinted genes Methylation remains after reprogramming Imprinting May result in both copies silenced or active Prader-Willi and Angelman syndrome both linked to the same imprinted region of chromosome 15 Some of the genes in this region are silenced in the egg At least one gene is silenced in the sperm Someone who inherits a defect on chromosome 15 is missing different active genes, depending on whether the chromosome came from mom or dad. Prader-Willi Syndrome Symptoms include learning difficulties, short stature, and compulsive eating Individuals are missing gene activity that normally comes from dad Happens when dad's copy is missing, or when there are two maternal copies Diagnosis DNA methylation testing Detects abnormal parent-specific imprinting on chromosome 15 70% deletion 15q11.2-q13 High resolution chromosomal studies FISH Sequencing Angelman Syndrome Symptoms include learning difficulties, speech problems, seizures, jerky movements, and an unusually happy disposition Happy expression and an unstable gait accompanied by uplifted arms Individuals are missing gene activity that normally comes from mom Happens when mom's copy is defective or missing, or when there are two paternal copies Beckwith-Wiedemann Syndrome Chromosome 11 gene when both are not methylated when only mother s should be Affected babies larger and taller in childhood but adults are normal height May be asymmetrical 10% increased risk of cancer in childhood Many undiagnosed 1 in 13,700 newborns worldwide I in 4000 in assisted reproduction 6

7 Silver-Russell Syndrome Retarded growth before and after birth and other symptoms associated with late development Chromosome 11 EGF2 gene is methylated in both parents Mouse Studies X-Chromosome Inactivation Epigenetic dosage compensation mechanism Lyon law lyonization is process by which one of the two x-chromosomes in females is inactivated Random inactivation occurs in embryo and inherited by all daughter cells Inactive X chromosome is heavily modified Low levels of histone acetylation High levels of methylation X inactivation 1. Cells from the normal female contain only one active X chromosome 2. X inactivation occurs early in development 3. Inactive X could be either maternally or paternally derived, and the inactivation would be random in any one cell 4. X inactivation irreversible in a somatic cell and all its descendants 7

8 Paradigm Shift Two Types of Epigenetics Context dependent Response to direct exposure: as long as environmental factor that bring about the epigenetic modification is present, the modification will manifest in each generation; may be reversible Germline-Dependent Mediated through germline. Modifications manifest in each generation in the absence of the causative agent. Imprint is transferred to subsequent generations and no therapeutic amelioration. Need 3 generations to demonstrate 8

9 Lead Evidence for Environmental Change of Phenotype: Agouti Mouse B12, folic acid, choline and betaine Epigentic Threats 9

10 Avon Longitudinal Study of Pregnancy and Childhood Past Exposures: Today s Epidemics Men who smoked regularly before the age of 11 had sons who had 5-10kg more body fat than their peers by the time they were in their teens Mothers who consume less fish during pregnancy have children with significantly lower IQs mothers who ate more than three portions of seafood a week during pregnancy had better neurological function Persistent depression during pregnancy can increase the chance of a child suffering developmental delay Depression in fathers was found to be associated with adverse emotional and behavioral outcomes in children aged 3.5 years Critical Windows for Germline Fetal germline Early childhood Males: pre-puberty: spermatogenesis Females: Peri-ovulation Peri-conception, to about week4 Transgenerational Disease Etiology Spermatogenic Defects >90% Male infertility ~10% Kidney disease ~30-40% Prostate disease ~50% Increase in mammary tumor formation ~10-20% Behavior 90% Ovarian Polycystic Ovarian Disease >90% Female premature pubertal onset >90% Obesity ~10-50% Our Mothers Exposures Progestins, Estrogenes, Corticosteroids to Prevent Miscarriage 10

11 Adverse Epigenetic Effects Jill Escher Autism Risks NOT Better awareness Vaccines Mild to moderate risk Fetal exposure to Anticonvulsants Antidepressants Thalidomide Pesticides, smog Perinatal complications including prematurity Perinatal age Maternal infection Most of the epidemic is unexplained Evidence Cancer Develops when a cell becomes abnormal and begins to grow out of control Can begin when mutation changes a cell's DNA sequence Cancer cells also have abnormal epigenomes Some genes are turned up and some are turned down -- often in the very same cells Activation of genes that promote cell growth Chromosome instability: highly active DNA is more likely to be duplicated, deleted, and moved to other locations Loss of imprinting 11

12 Hypermethylation of CpG Island Promotors Epigenetic Genetic Cancer and Aging Skin repeatedly exposed to the sun looks older than skin that hasn't because the skin's stem cells have had to divide more often to repair damage Epigenetic Alteration Drugs Inhibitors of DNA methyltransferases Deoxyazacytidine--decitabine Azacytidine Myelodysplastic syndrome Inhibitor of histone deacetylases Vorinostat Cutaneous T-cell lymphoma 12

13 How to Improve Your Epigenome Selenium and vitamin D status reduced the accumulation of epigenetic changes High blood folate and obesity increased them Men have more changes and more risk of colon cancer Polyphenol found in green tea could inhibit DNA methylation at specific cancer-related genes Diet low in glucose Diet Flavanol-rich diets Sulforaphane (found in broccoli) Curcumin (found in turmeric) Epigallocatechin gallate (found in green tea) Resveratrol (found in wine) Timing is vitally important Individualized Summary Epigenetics is study of how the genome is organized and managed Contrasting biological outcomes result from protein expression Mismanaged or disorganized epigenomes lead to disease Epigenome manipulation may have therapeutic value Conclusions Phenotype is result of complex geneenvironmental interactions Present, past and ancestral environments Disruption of epigenome leads to altered immune function Contributes to type 2 diabetes, CVD, RA, aging, cancer, etc. Improved understanding may lead to prevention and treatment 13

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