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

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unpublished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unpublished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unpublished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unpublished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
methylationmosaic

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 GeneticVariation Epigenetic Features
transcripts
dynamic
RNA-Sequencing Single Nucleotide Polymorphisms
Simple Sequence Repeats
DNA Methylation
Histone Modification
miRNA ExpressionExpression Microarrays
Amplified Fragment
Length Polymorphisms
Genomic
DataTypes
Data Tables
static
Gene Annotations Sequence Motifs
Gene OntologiesPathways
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