Role of Epigenetic Modification, Epigenetic Biomarkers and ...
Epigenetic and Environmental Influences on the Shellfish Immune Response
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Transcript of Epigenetic and Environmental Influences on the Shellfish Immune Response
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unpublished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unpublished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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Example
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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
Sharing
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
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