Epigenetic and Environmental Influences on the Shellfish Immune Response

Presentation given at the 1st International Conference of Fish and Shellfish Immunology. June 25-28, 2013. Vigo, Spain

Transcript

1. Epigenetic and Environmental Influences on the Shellfish Immune Response Steven B. Roberts Assistant Professor School of Aquatic and Fishery Sciences University of Washington Seattle - Washington - US
2. Open Science •You are free to Share! •Our lab practices open notebook science •Slides, links, and related material are available @ oystergen.es/vigo
4. Photo credit: Flickr, Creative Commons, dougbrown47
7. Immune Function e
9. Immune Function e
10. e Epigenetics Immune Function
12. e Immune Function
15. Temperature Genetics Reproductive Status Resources Culture Practices Salinity Pathogen
16. e Immune Function
17. e Characterization of genes involved in ceramide metabolism in the Pacific oyster (Crassostrea gigas). Timmins-Schiffman and Roberts 2012 Immune Function
18. e Rapid accumulation of an interleukin 17 homolog transcript in Crassostrea gigas hemocytes following bacterial exposure. Roberts et al 2008 Analysis of genes isolated from plated hemocytes of the Pacific Oyster, Crassostrea gigas. Roberts et al 2009 Characterization of genes involved in ceramide metabolism in the Pacific oyster (Crassostrea gigas). Timmins-Schiffman and Roberts 2012
19. e O c e a n A c i d i f i c a t i o n
20. e Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas. Gavery and Roberts 2012 Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas. Timmins-Schiffman et al 2012 O c e a n A c i d i f i c a t i o n
21. e Proteom e Immune Function O c e a n A c i d i f i c a t i o n
22. e O c e a n A c i d i f i c a t i o n unpublished Proteomic Response
23. e O c e a n A c i d i f i c a t i o n unpublished Proteomic Response oxidation reduction signal transduction oxidative stress response cellular stress & transport Elevated (7.2) Control (8)
24. e Immune Function
25. e Immune Function
26. e Immune Function
27. e unpublished Control
28. e unpublished Puta%ve  cytochrome  P450 Isocitrate  dehydrogenase  [NAD]  subunit  beta Alpha-­‐soluble  NSF  aCachment  protein C16orf62  homolog Radial  spoke  head  protein  4  homolog  A Flo%llin-­‐2 Small  nuclear  ribonucleoprotein-­‐associated  protein ES1  protein  homolog Sterile  alpha  and  TIR  mo%f-­‐containing  protein  1 Twinfilin-­‐2 Lachesin Syntaxin-­‐5 Serine  dehydratase-­‐like Caspase-­‐3 tRNA  methyltransferase  112  homolog Circularly  permutated  Ras  protein  1 Contac%n Caspase-­‐7 Apopto%c  chroma%n  condensa%on  inducer Calcium-­‐binding  protein Vacuolar  protein  sor%ng-­‐associated  protein  13C Cullin-­‐1 Control
29. e unpublished O c e a n A c i d i f i c a t i o n Control Elevated
31. e Immune Function Epigenetics
32. Photo credit: Flickr, Creative Commons, he-boden Epigenetics
33. Epigenetics
34. Histone Modification Epigenetics short RNAs DNA Methylation
35. Histone Modification Epigenetics short RNAs DNA Methylation m m
36. m m DNA Methylation
37. Function?
42. e Epigenetics Transcriptom e
43. traditional - vertebrate model Nature Reviews Genetics 9, 465-476 (June 2008) methylation
44. Non- Vertebrates?
45. Absent in several model organisms
46. Function? Shellfish?
47. mosaic associated with gene bodies Photo credit: Flickr, Creative Commons, dkeats
48. oyster mosaic associated with gene bodies
49. oyster mosaic associated with gene bodies methylation mosaic
50. Roberts and Gavery 2012 in silico analysis
51. Roberts and Gavery 2012 in silico analysis
52. Roberts and Gavery 2012 in silico analysis
53. relationship with function associated with gene bodies
54. Role?
55. Methylation Enhanced Random Variation theory
56. Biology
57. Biology
58. Biology In species that experience a diverse range of environmental conditions, processes have evolved to increase the number of potential phenotypes in a population in order to improve the chances for an individual’s survival.
59. M M M M M M M M M M germline methylation conventional transcription 5’ UTR promotor ubiquitously expressed, critical genes Transcriptional opportunities
60. x x M M M M sparse methylation alternative start sites sequence mutation change AA, premature stop codon conventional transcription transient methylation alternate transcript exon skipping tissue / temporal specific and inducible genes Transcriptional opportunities Roberts and Gavery 2012
61. DNA methylation in Crassostrea gigas Gill Sperm
62. DNA methylation in Crassostrea gigas Gill Sperm
63. If true? Limb Photo credit: Flickr, Creative Commons, csessums
64. Could change how we consider tolerance
65. Could change how we consider natural variation
66. Could change how we consider adaptation
68. defective methylation defective methylation
69. Profiling the DNA methylomes of plants exposed to bacterial pathogen, avirulent bacteria, or salicylic acid hormone revealed numerous stress-induced differentially methylated regions, many of which were intimately associated with differentially expressed genes.
70. ChIP-seq analysis of four histone modifications revealed that the priming treatment altered the epigenomic landscape; .... preferentially targeted transcription factors.
73. Open Science
74. Open Science web-native scholarship
75. Photo credit: Flickr, Creative Commons, speechless Sharing
76. How? Why?
77. Example
78. Example
79. Example
80. Example
81. Example unpublished
82. Example unpublished
84. Open Notebook Science ... there is a URL to a laboratory notebook that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. —Jean-Claude Bradley
85. Open Notebook Science
86. Open Notebook Science
87. Open Notebook Science
88. Open Notebook Science
89. Open Notebook Science Hello, I was doing a search for what concentrations of MgSO4 to use as a bivalve relaxant and came across Katie’s Notebook. What a cool idea! Please say thanks to Katie :). My boss said MgSO4 but most of the literature was MgCl2.... So g’day from the University of Queensland in Brisbane, Australia. Cheers KA email June 22, 2013
90. R e p r o d u c i b i l i t y usable data formats Sharing
91. R e p r o d u c i b i l i t y usable data formats Sharing Platforms FigShare Dryad GitHub runmycode
92. R e p r o d u c i b i l i t y usable data formats Sharing looking for patterns
93. Querying Disparate Datasets
98. Genome Primary Data Table Groupings Expressed Sequence Tags Gene Expression Genetic Variation Epigenetic Features transcripts dynamic RNA-Sequencing Single Nucleotide Polymorphisms Simple Sequence Repeats DNA Methylation Histone Modification miRNA Expression Expression Microarrays Amplified Fragment Length Polymorphisms Genomic Data Types Data Tables static Gene Annotations Sequence Motifs Gene Ontologies Pathways Orthologs Transposable Elements Interactions Other species genomes CpG statistics Structural Elements Size Growth Location Environment Stage Treatment Tissue Trait Strain Transcription Factors Binding Sites Publications
100. Immune Function e
101. Immune Function e I n s i g h t i n t o t h e C o m p l e x i t y
103. Acknowledgements Emma Timmins-Schiffman Mackenzie Gavery Claire Ellis Sam White Brent Vadopalas Bill Howe Dan Halperin EPA STAR Aquaculture Program Saltonstall-Kennedy acidification DNA methylation
104. Acknowledgements Emma Timmins-Schiffman Mackenzie Gavery Claire Ellis Sam White Brent Vadopalas Bill Howe Dan Halperin EPA STAR Aquaculture Program Saltonstall-Kennedy acidification DNA methylation oystergen.es/vigo