NSA Feb 2010: DNA Methylation Patterns & Epigenetic Regulation in the Pacific Oyster

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National Shellfisheries Association Annual Meeting

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NSA Feb 2010: DNA Methylation Patterns & Epigenetic Regulation in the Pacific Oyster

  1. 1. DNA Methylation Patterns & Epigenetic Regulation in the Pacific Oyster <br />Mackenzie Gavery & Steven Roberts<br />University of Washington<br />School of Aquatic and Fishery Sciences<br />
  2. 2. Outline<br /><ul><li>Background: epigenetics, DNA methylation
  3. 3. Results: characterization of DNA methylation in Pacific oysters
  4. 4. Implications
  5. 5. Future directions</li></li></ul><li>Background: <br />color<br />disease resistance<br />growth<br />TRAITS<br />pathogens<br />toxins<br />nutrition<br />ENVIRONMENT<br />GENES (DNA)<br />
  6. 6. Background: <br />color<br />disease resistance<br />growth<br />TRAITS<br />pathogens<br />toxins<br />nutrition<br />EPIGENOME<br />(DNA methylation)<br />ENVIRONMENT<br />GENES (DNA)<br />
  7. 7. Background: <br />color<br />disease resistance<br />growth<br />TRAITS<br />pathogens<br />toxins<br />nutrition<br />EPIGENOME<br />(DNA methylation)<br />ENVIRONMENT<br />GENES (DNA)<br />
  8. 8. Epigenetics <br />Heritable changes in trait or phenotype, caused by a mechanism other than mutation to the DNA sequence<br />Most well understood epigenetic mechanism is DNA methylation:<br /><ul><li>occurs at CpG sites in animals
  9. 9. regulates gene expression
  10. 10. influenced by the environment </li></ul>Me<br />C<br />G<br />G<br />C<br />
  11. 11. DNA methylation<br />Effects of disruptions:<br />tumor promotion<br />alteration of development<br />inhibition of reproduction<br />Compounds that impact normal epigenetic functions:<br />Endocrine disruptors: estrogen, BPA, pesticides<br />
  12. 12. Characterization of DNA methylation in Pacific oysters:<br />describe distribution of methylation<br />elucidate functional significance<br />
  13. 13. Results<br />Methylation Specific PCR<br />Bisulfite sequencing<br />In silicoanalysis<br />
  14. 14. Results<br />Methylation Sensitive PCR<br />Bisulfite sequencing<br />In silicoanalysis<br />
  15. 15. Results: gene-targeted approach<br />Methylation Sensitive PCR<br />5 stress related genes were examined<br />Identified CpG methylation in heat shock protein 70<br />Bisulfite sequencing<br />136 bp fragment: 1 of 7 CpG methylated (homology to neuromedin-u receptor)<br />93 bp fragment: 1 of 2 CpG methylated (homology to bromodomain adjacent to zinc finger domain)<br />
  16. 16. Results<br />Methylation Sensitive PCR<br />Bisulfite sequencing<br />In silicoanalysis<br />
  17. 17. Results<br />Methylation Sensitive PCR<br />Bisulfite sequencing<br />In silicoanalysis<br />predicted methylation status of 12,000 C. gigas sequences from GigasBase<br />sequences were grouped by Gene Ontology term<br />an average predicted methylation status was determined<br />
  18. 18. Regulation of Gene Expression<br />low<br />mid<br />high<br />Predicted DNA Methylation<br />
  19. 19. Regulation of Gene Expression<br />low<br />mid<br />high<br />Predicted DNA Methylation<br />
  20. 20. Implications:<br />evidence suggests DNA methylation plays a regulatory role in Pacific oysters<br />implications for immune/stress responses<br />
  21. 21. Implications: Environment<br /> LowHigh<br />
  22. 22. Implications: Selective Breeding<br />Selective breeding can contribute to improved & predictable performance in oysters<br />Understanding geneticand epigenetic influences will increase predictability<br />
  23. 23. Implications: Hybrid Vigor<br />Heterosis (hybrid vigor)<br />mechanism not fully understood<br />epigenetic mechanisms have been proposed<br />better understanding will allow for greater control in predicting and manipulating gene expression in oysters <br />X<br />=<br />
  24. 24. Implications: Nutrition<br /><ul><li>diet can modify traits by affecting DNA methylation. </li></ul>Waterland & Jirtle, Molecular and Cellular Biology, 2003<br />
  25. 25. Future Directions<br />Method evaluation/development:<br />challenges associated with non-model species<br />new approaches:<br />Whole genome bisulfite sequencing (BS-seq)<br />Methylated DNA immunoprecipitation (MeDIP)<br />MeDIP-seq<br />MeDIP-chip<br />
  26. 26. Summary<br />Characterization of DNA methylation in Pacific oyster suggests a role in gene regulation, specifically genes with inducible expression<br />DNA methylation could be an important mechanism contributing to phenotypic variation in oysters <br />Important evaluate & develop methods and tools to evaluate epigenetic mechanisms in bivalves<br />
  27. 27. Acknowledgements<br />UW, SAFS<br />Dr. Steven Roberts<br />Samuel White<br />Lisa Crosson<br />Emma Timmins-Schiffman<br />Taylor Shellfish Farms<br />Joth Davis<br />NSA-PCS <br />NOAA Aquaculture Program<br />

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