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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Immune Function

disease resistance

Immune Function

disease resistance

disease resistance

Epigenetics

Immune Function

disease resistance

Immune Function

TemperatureGenetics

Reproductive Status

Resources

Culture Practices

Salinity

Pathogen

disease resistance

Immune Function

disease resistance

Characterization of genes involved in ceramide metabolism in the Pacific oyster (Crassostrea gigas).Timmins-Schiffman and Roberts 2012

Immune Function

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

disease resistance

O c e a n A c i d i f i c a t i o n

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

disease resistance

Proteome

Immune Function

O c e a n A c i d i f i c a t i o n

disease resistance

O c e a n A c i d i f i c a t i o nunpublished

Proteomic Response

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)

disease resistance

Immune Function

disease resistance

Immune Function

disease resistance

Immune Function

disease resistance

unpublished

Control

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unpublished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

disease resistance

unpublishedO c e a n A c i d i f i c a t i o n

Control Elevated

disease resistance

Immune Function

Epigenetics

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Epigenetics

Epigenetics

Histone Modification

Epigenetics

short RNAs

DNA Methylation

Histone Modification

Epigenetics

short RNAs

DNA Methylation

m

m

m

m

DNA Methylation

Function?

disease resistance

Epigenetics

Transcriptome

traditional - vertebrate model

Nature Reviews Genetics 9, 465-476 (June 2008)

methylation

Non-Vertebrates?

Absent in severalmodel

organisms

Function?Shellfish?

mosaic

associated with gene bodies

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oyster

mosaic

associated with gene bodies

oyster

mosaic

associated with gene bodies

methylationmosaic

Roberts and Gavery 2012

in silico analysis

Roberts and Gavery 2012

in silico analysis

Roberts and Gavery 2012

in silico analysis

relationshipwith

functionassociated with gene bodies

Role?

MethylationEnhancedRandomVariationtheory

Biology

Biology

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.

M M M M M M M M M M

germline methylation

conventional transcription5’ UTR promotor

ubiquitously expressed, critical genes

Transcriptional opportunities

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

DNA methylation in Crassostrea gigas

Gill

Sperm

DNA methylation in Crassostrea gigas

Gill

Sperm

If true?

Limb

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Could change how we consider tolerance

Could change how we consider natural variation

Could change how we consider adaptation

defectivemethylation

defectivemethylation

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.

ChIP-seq analysis of four histone modifications

revealed that the priming treatment altered the

epigenomic landscape; .... preferentially targetedtranscription factors.

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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

R e p r o d u c i b i l i t yusable data formats

Sharing

R e p r o d u c i b i l i t yusable data formats

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PlatformsFigShareDryadGitHubrunmycode

R e p r o d u c i b i l i t yusable data formats

Sharing

looking for patterns

Querying Disparate Datasets

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

Immune Function

disease resistance

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

Acknowledgements

Emma Timmins-Schiffman

Mackenzie GaveryClaire Ellis

Sam WhiteBrent Vadopalas

Bill HoweDan Halperin

EPASTAR

Aquaculture Program

Saltonstall-Kennedyacidification

DNA methylation

Acknowledgements

Emma Timmins-Schiffman

Mackenzie GaveryClaire Ellis

Sam WhiteBrent Vadopalas

Bill HoweDan Halperin

EPASTAR

Aquaculture Program

Saltonstall-Kennedyacidification

DNA methylation

oystergen.es/vigo