Epigenetic and Environmental Influences on the Shellfish Immune Response
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Epigenetic and Environmental Influences on the Shellfish Immune Response
Steven B. RobertsAssistant Professor
School of Aquatic and Fishery SciencesUniversity of Washington
Seattle - Washington - US
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Photo credit: Flickr, Creative Commons, dougbrown47
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Immune Function
disease resistance
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Immune Function
disease resistance
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disease resistance
Epigenetics
Immune Function
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disease resistance
Immune Function
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TemperatureGenetics
Reproductive Status
Resources
Culture Practices
Salinity
Pathogen
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disease resistance
Immune Function
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disease resistance
Characterization of genes involved in ceramide metabolism in the Pacific oyster (Crassostrea gigas).Timmins-Schiffman and Roberts 2012
Immune Function
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disease resistance
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
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disease resistance
O c e a n A c i d i f i c a t i o n
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disease resistance
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
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disease resistance
Proteome
Immune Function
O c e a n A c i d i f i c a t i o n
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disease resistance
O c e a n A c i d i f i c a t i o nunpublished
Proteomic Response
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disease resistance
O c e a n A c i d i f i c a t i o nunpublished
Proteomic Response
oxidation reduction
signal transduction
oxidative stress response
cellular stress & transport
Elevated (7.2) Control (8)
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disease resistance
Immune Function
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disease resistance
Immune Function
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disease resistance
Immune Function
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disease resistance
unpublished
Control
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disease resistance
unpublished
Puta%ve cytochrome P450Isocitrate dehydrogenase [NAD] subunit betaAlpha-‐soluble NSF aCachment proteinC16orf62 homologRadial spoke head protein 4 homolog AFlo%llin-‐2Small nuclear ribonucleoprotein-‐associated proteinES1 protein homologSterile alpha and TIR mo%f-‐containing protein 1Twinfilin-‐2LachesinSyntaxin-‐5Serine dehydratase-‐likeCaspase-‐3tRNA methyltransferase 112 homologCircularly permutated Ras protein 1Contac%nCaspase-‐7Apopto%c chroma%n condensa%on inducerCalcium-‐binding proteinVacuolar protein sor%ng-‐associated protein 13CCullin-‐1
Control
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disease resistance
unpublishedO c e a n A c i d i f i c a t i o n
Control Elevated
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disease resistance
Immune Function
Epigenetics
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Photo credit: Flickr, Creative Commons, he-boden
Epigenetics
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Epigenetics
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Histone Modification
Epigenetics
short RNAs
DNA Methylation
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Histone Modification
Epigenetics
short RNAs
DNA Methylation
m
m
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m
m
DNA Methylation
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Function?
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disease resistance
Epigenetics
Transcriptome
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traditional - vertebrate model
Nature Reviews Genetics 9, 465-476 (June 2008)
methylation
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Non-Vertebrates?
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Absent in severalmodel
organisms
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Function?Shellfish?
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mosaic
associated with gene bodies
Photo credit: Flickr, Creative Commons, dkeats
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oyster
mosaic
associated with gene bodies
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oyster
mosaic
associated with gene bodies
methylationmosaic
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Roberts and Gavery 2012
in silico analysis
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Roberts and Gavery 2012
in silico analysis
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Roberts and Gavery 2012
in silico analysis
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relationshipwith
functionassociated with gene bodies
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Role?
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MethylationEnhancedRandomVariationtheory
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Biology
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Biology
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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.
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M M M M M M M M M M
germline methylation
conventional transcription5’ UTR promotor
ubiquitously expressed, critical genes
Transcriptional opportunities
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x x
M M M Msparse methylation
alternative start sites
sequence mutationchange AA, premature stop codon
conventional transcriptiontransient methylation
alternate transcriptexon skipping
tissue / temporal specific and inducible genes
Transcriptional opportunities
Roberts and Gavery 2012
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DNA methylation in Crassostrea gigas
Gill
Sperm
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DNA methylation in Crassostrea gigas
Gill
Sperm
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If true?
Limb
Photo credit: Flickr, Creative Commons, csessums
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Could change how we consider tolerance
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Could change how we consider natural variation
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Could change how we consider adaptation
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defectivemethylation
defectivemethylation
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Profiling the DNA methylomes of plants exposedto bacterial pathogen, avirulent bacteria, or salicylic acid
hormone revealed numerous stress-induced differentially methylated regions, many of which
were intimately associated with differentiallyexpressed genes.
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ChIP-seq analysis of four histone modifications
revealed that the priming treatment altered the
epigenomic landscape; .... preferentially targetedtranscription factors.
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Open Science
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Open Science
web-native scholarship
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Sharing
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How?
Why?
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Example
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Example
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Example
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unpublished
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Example
unpublished
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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
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Open Notebook Science
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Open Notebook Science
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Open Notebook Science
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Open Notebook Science
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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.CheersKA
email June 22, 2013
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R e p r o d u c i b i l i t yusable data formats
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PlatformsFigShareDryadGitHubrunmycode
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R e p r o d u c i b i l i t yusable data formats
Sharing
looking for patterns
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Querying Disparate Datasets
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Genome
Primary Data Table Groupings
Expressed Sequence Tags
Gene Expression Genetic Variation Epigenetic Features
transcripts
dyna
mic
RNA-Sequencing Single Nucleotide Polymorphisms
Simple Sequence Repeats
DNA Methylation
Histone Modification
miRNA ExpressionExpression Microarrays
Amplified FragmentLength Polymorphisms
Gen
omic
D
ata
Type
s
Data Tables
stat
ic
Gene Annotations Sequence Motifs
Gene OntologiesPathwaysOrthologs
Transposable Elements
Interactions
Other species genomes
CpG statistics
Structural Elements
SizeGrowthLocation
EnvironmentStage
TreatmentTissueTraitStrain
Transcription Factors Binding Sites
Publications
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Immune Function
disease resistance
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Immune Function
disease resistance
I n s i g h ti n t ot h e
C o m p l e x i t y
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Acknowledgements
Emma Timmins-Schiffman
Mackenzie GaveryClaire Ellis
Sam WhiteBrent Vadopalas
Bill HoweDan Halperin
EPASTAR
Aquaculture Program
Saltonstall-Kennedyacidification
DNA methylation
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Acknowledgements
Emma Timmins-Schiffman
Mackenzie GaveryClaire Ellis
Sam WhiteBrent Vadopalas
Bill HoweDan Halperin
EPASTAR
Aquaculture Program
Saltonstall-Kennedyacidification
DNA methylation
oystergen.es/vigo
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