Genome Duplication and Fish Models for Toxicology · • Genome duplication in vertebrates zebrafish coelacanth bony fish Two rounds of genome duplication jawed vertebrates gar xenopus

DIVISION OF COMPARATIVE MEDICINE

~\. National Institute of Environmental Health Sciences liilllr'J' Your Environment. Your Health. ,'~ National Toxicology Program ~ U.S. Department of Health and Human Services

Genome duplication and fish models for toxicology

John Postlethwait University of Oregon

NIH ' DIVISION OF COMPARATIVE MEDICINE

··-·• ~\. Nationa_l Institute of En~ir~nmental Hea~~S · -lilllr'/ Your Environment. Your Health. ciences

Genome duplication and fish models for toxicology Frank von Hippel N AZ U

Loren Buck N AZ U

Tom Titus UO

Pete Batzel UO

Jesse Gologergen Sivuqaq Island

Tiffany Immingen Sivuqaq Island

Ingo Braasch

The problem: People living a subsistence lifestyle in the Arctic are highly exposed to persistent organic pollutants.

Annie Alowa, Sivuqaq Islander

' ~""' ,;

t@~ a 1 VA ,. . ... -). _ . ..··~i ·t. • . .A. · . . • ··.•~--... ~. .. ,•· ·••' ... . . 1 11 . ·•. . . ' . . •' '• • \ . . . . .

. 'II,_ !'· . • ·•. -~ ... • • .• : ,.

~''-~--.. ----. \-:l·· 4_· ..... . -:

····: ... : . ··. "\ .:· . : ·- . ·~ :- - ---

aqumaps.org

organochlorines evaporate

move to colder climates

condense & fall

Biological magnification

The problem: Formerly used defense sites

Greenland

Canada Norway

SLIGlobal distillation Point sources Sources:

' ' ~,v- ,;

t@.,- ~ : 1 VA ,. . ·. -:·J. . • !

... ... . . . .. ··~ : 1.. a·· •· .A . ·· •

• \ I •• •• :• .' • · ••' .:• • • • . . . ' . . .. , . . . . . •. . . . . . . . ~.... . •. ·• .. · .. . :.:, ~- \ ... . ' ... ;.-.~. ... I . :l ... ... • 4_· . -:· ~ _;· ~,. fyl ______ ..:,

aqumaps.org

Global distillation

Biological magnification

The problem: Formerly used defense sites

Greenland

Canada Norway

SLI Point sources

9-spine stickleback

Teleost fish are convenient models for toxicology.

How to connect teleost genomes to human biology?

• Genome duplication complicates connectivity • Genome duplication in vertebrates


• Ohnologs gone missing and lineage-specific evolution • Application: St. Lawrence Island

How to connect teleost genomes to human biology? • Genome duplication in vertebrates

zebrafish

bony fish Susumo Ohno

Evolution by Gene Two rounds of genome Duplication (1970)duplication

Ohnologs: duplicates from genome duplication

jawed vertebrates

1 Hox cluster

4 Hox clusterse shark cartilaginous fish

How to connect teleost genomes to human biology? zebrafish

e shark

bony fish

cartilaginous fish

jawed vertebrates

coelacanth

xenopus

chicken

mouse

human

• Genome duplication in vertebrates

rayfin fish

Two rounds of genome duplication

lobefin fish

1 Hox cluster

4 Hox clusters

rayfin fish

teleost fish



zebrafish

coelacanth

e shark

bony fish

cartilaginous fish

jawed vertebrates

gar

xenopus

chicken

mouse

human

medaka

cavefish

goldeye

eel


lobefin fish

1 Hox cluster

4 Hox clusters


4 Hox clusters

1 Hox cluster

human

4 Hox clusters


zebrafish

coelacanth

bony fish


jawed vertebrates

gar

xenopus

chicken

mouse

medaka

cavefish

goldeye

eel

Teleost genome duplication

1R, 2R VGD

3R, TGD

e shark cartilaginous fish

teleost fish

rayfin 7-8 Hox clusters Amores…

Postlethwait 1998 Science

fish

Amores…Postlethwait 2011 Genetics

lobefin fish

4 Hox clusters

teleost fish 7-8 Hox clusters

Spotted gar: • Diverged before the TGD • Biology similar to zebrafish


zebrafish

coelacanth

e shark 4 Hox clusters

bony fish

cartilaginous fish

1 Hox cluster


jawed vertebrates

gar

xenopus

chicken

mouse

human

medaka

cavefish

goldeye

eel



1R, 2R VGD

3R, TGD


4 Hox clusters What does duplication mean for toxicology?

4 Hox clusters

teleost fish 7-8 Hox clusters

Spotted gar: • Diverged before the TGD • Biology similar to zebrafish

• Genomics similar to tetrapods • Same duplication as human

• Amenable to laboratory culture • Can grow from embryos


zebrafish

coelacanth

e shark

bony fish

cartilaginous fish

1 Hox cluster


jawed vertebrates

gar

xenopus

chicken

mouse

human

medaka

cavefish

goldeye

eel


1R, 2R VGD

3R, TGD

What does duplication mean for toxicology?


1R, 2R VGD


chicken

mouse

human

jawed vertebrates

1 Hox cluster e shark cartilaginous fish

zebrafish

coelacanth

bony fish gar

xenopus

medaka

cavefish

goldeye

eel



3R, TGD

cytoplasm

nucleus

dioxin response element

dioxins

AHR

cyp1a1

ARNTAHR

Catchen…Postlethwait 2009 Genome Res. 19:1497

Arnt Arntl Tandem duplication

VGD1 Arnt Arntl

Arnt Arntl

VGD2 Arnt Arntl

Arnt2 Arntl2

TGD

arnt arntl1a

arntl1b

arnt2 arntl2zebrafish

human

cytoplasm

nucleus


dioxins

AHR

cyp1a1

ARNTAHR

How do we know?


ARNT ARNTL

ARNT2 ARNTL2

What does duplication mean for toxicology?

100

,-----Hsa.ARNTI. ---Dre.amtl1a

---Dre.amtl1b r--------Hsa.ARNTL2

100 '--------Dre.amt12 ,__ ____ -Rfl .110703

,-----Hsa.ARNT2 ,...... __ --l

81

Dre.amt2

,--------Hsa.ARNT

~-----Dre.amt

How do we know?

gene tree How to connect teleost genomes to human biology?

arnt arntl1a



VGD1 Arnt Arntl

Arnt Arntl

VGD2 Arnt Arntl

Arnt2 Arntl2

TGD zebrafish

human

Arnt4 Arntl4

Arnt3 Arntl3

ARNT ARNTL

ARNT2 ARNTL2

arnt2 arntl1b

arnt2 arntl2

arnt2b arntl2b

orthologs

100



100 '--------Dre.amt12 ,__ ____ -Rfl .110703

,-----Hsa.ARNT2 ,...... __ --l

81

Dre.amt2

,--------Hsa.ARNT

~-----Dre.amt

How do we know?


TGD

arnt arntl1a

arntl1b

arnt2 arntl2



VGD1 Arnt Arntl

Arnt Arntl

VGD2 Arnt Arntl

Arnt2 Arntl2

zebrafish

human

ARNT ARNTL

ARNT2 ARNTL2

orthologs

100

100



'--------Dre.amt12 ,__ ____ -Rfl .110703

,-----Hsa.ARNT2 ,...... __ --l

81

Dre.amt2

,--------Hsa.ARNT

~-----Dre.amt

How do we know?


VGD1 Arnt Arntl

Arnt Arntl Arnt ArntlTandem duplication

TGD

arnt arntl1a

arntl1b

arnt2 arntl2

VGD2 Arnt Arntl

Arnt2 Arntl2

zebrafish

human

ARNT ARNTL

ARNT2 ARNTL2

orthologs


100


---Dre.amtl1b

100 '--------Dre.amt12 ,__ ____ -Rfl .110703

,-----Hsa.ARNT2 ,...... __ --l

81

Dre.amt2

,--------Hsa.ARNT

~-----Dre.amt

human

TGD

arnt arntl1a

arntl1b

arnt2 arntl2zebrafish

ARNT ARNTL

ARNT2 ARNTL2

Arnt Arntl

VGD1 Arnt Arntl

Arnt Arntl

VGD2 Arnt Arntl

Arnt2 Arntl2

How do we know?


gene tree

Tree shows duplication after human-fish divergence.

co-orthologs

Tandem duplication


ARNTLarntl1b

arntl1a

conserved syntenies

human-fish

show duplicated chromosome segments

How do we know?

How to connect teleost genomes to human biology? Tree shows duplication after

arnt arntl1adivergence.

arnt2 arntl1b

arnt2 arntl2 TGD

arnt2b arntl2b

zebrafish

VGD1 Arnt Arntl VGD2 Arnt Arntl

Arnt Arntl Arnt2 Arntl2

Arnt4 Arntl4

Arnt3 Arntl3

Arnt Arntl Tandem duplication ARNT ARNTL

human ARNT2 ARNTL2How do we know?


♦

+ +-++t++ + +♦ + -· ++++ + ♦ + + ++ + ♦++ + +

+ + ·- -*• + + ♦ + ♦

+ * + + ♦ ++ ++

+ + + ... +

+ + + + ++-I+ ♦++ + + + ++ +

+ ++ ..... + + + ..... + ++

+ -++- ++++ * ++ ♦

+ ++ ++ + +

++ +

. +- _ __.._ ··- - -- -➔ -++- .. -+- ·+-·- ·- .... - - .,_.,... __ +-·

++ ♦ ♦ + +++ -· ** + + + +

+ - +

0 + + + HI-++ + ++

♦

+ + + + + + ++• + + + + + +

+ + + + + + + + - + + + + ............ +++++ + ·- .... + + + ... + ♦ ♦- +

How do we know? ARNT

How to connect teleost genomes to human biology?Human

chromosomes Duplicated ARNTL chromosome

segments in arnt arntl1aARNTL2 humanARNT2 genome arnt2 arntl1b

ARNT2 ARNTL2

arnt2 arntl2 Genes on human chromosome 11


Arnt4 Arntl4

Arnt3 Arntl3

TGD

arnt2b arntl2b

zebrafish

human


Arnt Arntl Tandem duplication ARNT ARNTL

How do we know?


♦

+ +-++t++ + +♦ + -· ++++ + ♦ + + ++ + ♦++ + +

+ + ·- -*• + + ♦ + ♦

+ * + + ♦ ++ ++

+ + + ... +

+ + + + ++-I+ ♦++ + + + ++ +

+ ++ ..... + + + ..... + ++

+ -++- ++++ * ++ ♦

+ ++ ++ + +

++ +

. +- _ __.._ ··- - -- -➔ -++- .. -+- ·+-·- ·- .... - - .,_.,... __ +-·

++ ♦ ♦ + +++ -· ** + + + +

+ - +

0 + + + HI-++ + ++

♦

+ + + + + + ++• + + + + + +

+ + + + + + + + - + + + + ............ +++++ + ·- .... + + + ... + ♦ ♦- +

How do we know? ARNT

How to connect teleost genomes to human biology?Human

chromosomes Duplicated ARNTL chromosome How do

ARNTL2 ARNT2

Genes on human chromosome 11



How do we know?


Arnt4 Arntl4

Arnt3 Arntl3


ARNT ARNTL

ARNT2 ARNTL2

TGD

arnt arntl1a

arnt2 arntl1b

arnt2 arntl2

arnt2b arntl2b

zebrafish

human

segments in human genome

• Genome duplication complicates connectivity

fish genes relate to human genes?




Regulatory duplication


Protein coding Functional domains

nonfunctionalization Gene loss: most frequent fate

Alan Force

Force…Postlethwait 1999 Genetics


Protein coding Functional domains

Regulatory

nonfunctionalization neofunctionalization subfunctionalization

duplication

Gene loss: most New functions evolve Reciprocal loss of frequent fate from ancestral genes ancestral functions

Alan Force


•. -L

..... -• -L

• -L ••

•-/ .

--L ••

--L •• t ••

neofunctionalization New functions evolve from ancestral genes

nonfunctionalization Reciprocal loss of ancestral functions

Gene loss: most frequent fate

subfunctionalization

Protein coding


duplication

Species Retained TGD pairs

Codingge n e s

%retained

Zebrafish 2,228 26,459 8.4

Stickleback 2,156 20,787 10.4

Medaka 1,910 19,699 9.7

Te t r a od o n 1,853 19,602 9.5

Functional domains

Most teleost genes are 1:1 orthologs with human

Alan ForceWe don’t yet know the relative importance of these fates.


• Genome duplication complicates connectivity Species Retained TGD Coding %retained

pairs genes Zebrafish 2,228 26,459 8.4

Stickleback 2,156 20,787 10.4

Medaka 1,910 19,699 9.7

Tetraodon 1,853 19,602 9.5

What does this mean for toxicology?

Problem: All can occur in a lineage-specific fashion.

nonfunctionalization neofunctionalization subfunctionalization Gene loss: most New functions evolve Reciprocal loss of frequent fate from ancestral genes ancestral functions

Alan ForceWe don’t yet know the relative

Forceimportance of these fates.

…Postlethwait 1999 Genetics


cytoplasm

nucleus


dioxins

AHR

cyp1a1

ARNTAHRAHR

promotes expression of oxygen-responsive genes.

What about AHR?

Amphioxus

neofunctionalization subfunctionalization

To see if this is subfunctionalization or neofunctionalization, must look at a pre-duplication outgroup.


heterodimer with ligand- heterodimer with CLOCK, bound AHR, promotes promotes expression of expression of xenobiotic circadian rhythm genes metabolism genes

ARNT ARNTL

ARNT2 ARNTL2 heterodimer with hypoxia- heterodimer with inducible factor 1alpha, CLOCK & HIF1alpha

Ascidians Appendicularians http://marineinvaders.myspecies.info/taxonomy/term/70 evodevogenomics-unibarcelona.weebly.com/oikopleura www2.le.ac.uk/departments/geology/people/goodall-r/personal/images/lancelet.

https://evodevogenomics-unibarcelona.weebly.com/oikopleura

http://marineinvaders.myspecies.info/taxonomy/term/70

Dre16

Gga2

Dre22

Gga7


nonfunctionalization subfunctionalizationneofunctionalization

cytoplasm

nucleus


dioxins AHR

cyp1a1

AHR ARNT

What about AHR?

AHR

Dre16 Dre22

one AHR gene

three AHR-related genes

three AHR-related genes

Conserved syntenies show that chicken and zebrafish AHR-related genes are orthologs

How did AHR-related genes evolve?Karchner 2005 Biochem J. 392:153

VGD2 ahr2 ahr1b

ahr1a ahr1b’ahr ahr2 ahr1

ahr2 ahr1b

ahr1a ahr1b’

AHR2 AHR1B

AHR ahr1b’

ahr1b’AHR

ahr1bahr1a

How did AHR-related genes evolve?

cytoplasm

nucleus


dioxins AHR

cyp1a1

AHR ARNT

TGD zebrafish

human

chicken


Zebrafish three AH Rs • AHR2 primary mediator of toxicity ~ - =----• AHRl A deficient in TCDD binding and • transactivation activity • AHRl B functiona l but no known toxicological

roles


cytoplasm

nucleus


dioxins AHR

cyp1a1

AHR ARNT

Robert Tanguay Oregon State University 2018 10 25


VGD2 ahr2 ahr1b

ahr1a ahr ahr2 ahr1

ahr2 ahr1b

ahr1a

AHR2 AHR1B

AHR

AHR

TGD zebrafish

human

chicken

The ‘primary mediator of toxicity’ for teleosts is not the ortholog of human AHR

Zebrafish ortholog of human AHR is an ‘incipient pseudogene’. Karchner 2005 Biochem J. 392:153

Zebrafish three AH Rs • AHR2 primary mediator of toxicity • AHRl A deficient in TCDD binding and • transactivation activity • AHRl B functiona l but no known toxicological

roles


cytoplasm

nucleus


dioxins AHR

cyp1a1

AHR ARNT

Robert Tanguay Oregon State University 2018 10 25


VGD2 ahr2 ahr1b


ahr2 ahr1b

ahr1a ahr1b’

AHR2 AHR1B

AHR ahr1b’

ahr1b’AHR

ahr1bahr1a

TGD zebrafish

human

chicken

Study of ahr1b may reveal sub-functions of human AHR gene

subfunctionalization

VGD2 ahr2 ahr1b


ahr2 ahr1b

ahr1a ahr1b’

AHR2 AHR1B

AHR ahr1b’

ahr1b’AHR

ahr1bahr1a


cytoplasm

nucleus


dioxins AHR

cyp1a1

AHR ARNT

TGD zebrafish

human

chicken


Postlethwait 2007 J Exp Zool B Mol Dev Evol. 308:563

• Ohnologs gone missing and lineage-specific evolution




St. Lawrence Island AlaskaRussia

• Application: St. Lawrence Island

Savunga

St. Lawrence Island

Northeast Cape

Alaska Russia

air strip

Main operations of FUD

Suqitughneq River

12 10

14

11 13

8 7

6

5 4

2

3 • Application: St. Lawrence Island

1985 - 2014, $120M spent on remediation

air strip

Main operations of FUD

Suqitughneq River

12 10

14

11 13

8 7

6

5 4

2

3 • Application: St. Lawrence Island

1985 - 2014, $120M spent on remediation

Do upstream and downstream fish differ?

w en

+f 0 0) 0 0) ,-

.s ~ IIl 0 e:. ro § C: 0 ~ lO

::E

0

2 Estuary

i i 3 4 5 0 7 8

Site number

=> significantly more PCBs in downstream fish

Alaska blackfish

12 10

14

11 13

8 7

6

5 4

2

3

Are PCBs from global distillation or the FUD?

Do upstream and downstream fish differ?

von Hippel 2018 Environmental Pollution 234:279

0000 00 00 00 0

0 0 0 000 00000000 0 0000000000000 000000000 0 000000000 000 0 0 0000 0000000 000000000000 0 0000 0000

Are PCBs from global distillation or the FUD? 3

Greater => Upstream from global distillationupstream => Downstream PCBs from FUD + distillation. Greater light heavydown stream

6

7 8 12

10 11 13

14 Main operations of FUD

Danielle Dillon What are the biological effects?

What are the biological effects? sex genotype PCR Gene expression differences?

4 females from highly contaminated sites 4 females from less contaminated sites

BIOO NEXTflex qRNA-seq

Strand-specific: guards against gDNA

Unique molecular indexes: guards against PCR duplicates

Tom Titus UO

■ --

brca2 paired-end reads Aligned 9-spine reads to 3-spine genome

3-spine genome 3’UTR unannotated

polymorphisms

9-spine PCBs low strand specific

wrong way => genomic contamination

9-spine PCBs high

Pete Batzel

■ --I I

3-spine genome

brca2

DESeq2: Finds differentially expressed genes

paired-end reads

Pete Batzel

Aligned 9-spine reads to 3-spine genome

9-spine PCBs low

9-spine PCBs high

compared to

Differentially expressed genes Females: contamin/uncontam 2312 Males: contamin/uncontam 642

What do these genes do?

DAVID 6.7: Database for Annotation, Visualization and Integrated Discovery

DESeq2: Finds differentially expressed genes

Annotation Cluslllr1 Enrichment Sc:otr.15.17 k, Cowit P _Value BenJamlnl

UP _KEYWORDS Cell cycle RT - 135 1.9E-20 S.2E-l8

UP _KEYWORDS Cell division 9 1 1.2E-17 l.7E-l5

UP _KEYWORDS Mitosis ..... - 69 3.7E-16 3.0E-14

GOTERM_BP _DIRECT cell division RT - 83 1. l E-13 2.6E-10

What do these genes do? DAVID 6.7: brca2 (fancd1) = down cdc23 = down fbxo5 = down cell cycle genes h2ax = down haus6 = down mad2l1 = down rab11fip4a = down llgl2 = down ccnb1 = down most tgf betas down


UP _KEYWORDS Cell cycle RT - 135 1.9E-20 S.2E-l8

UP _KEYWORDS Cell division RT - 9 1 1.2E-17 l.7E-l5

UP _KEYWORDS Mitosis RT - 69 3.7E-16 3.0E-14


GOTERM_BP _DIRECT mitotic nuclear division RT • 63 1.SE-11 2.3E-8

Annotation Clusta, 2 Enrichment Scorw: 11.1, Ill,, Cowit P _Value B■nJ■mlnl

UP _KEYWORDS

GOTERM_BP _DIRECT

- - --~-------- ii

ii

'UI 1 ""'-'" Q RE-14

E-8

What do these genes do? brca2 (fancd1) = down cdc23 = down fbxo5 = down h2ax = down haus6 = down

DNA replication genes

mcm3,4,6,7 cdc45 hsc70 pcna rbbp4 tert terf1, terf2

mad2l1 = down rab11fip4a = down llgl2 = down ccnb1 = down most tgf betas down


UP _KEYWORDS Cell cycle RT - 135 1.9E-20 5.2E-l8

UP _KEYWORDS Cell division RT - 91 1.2E-17 l.7E-l5


GOTERM_BP _DIRECT cell division RT - 83 1. lE-13 2.6E-10

GOTERM_BP _DIRECT mitotic nuclear division RT • 63 1.5E-11 2.3E-8


UP _KEYWORDS

GOTERM_BP _DIRECT

GOTERM_BP _DIRECT

D A replication

Gl/5 transit ion of mitot ic cell cycle

D A replication ini iation

ii

ii

i

38

36

19

1.5E-15 9.8E-l4

3.lE-11 3.7E-8

1. 3E-10 l.2E-7

Annotation Cluslllr 3 Enrichment Score: 8.IM k, Cowit . P _ Value BenJ■mlnl

UP _KEYWORDS

UP _KEYWORDS

AT 67

58

4 . 4E-9 l.8E-7

1 .8E-8 5.4E-7

What do these genes do? brca2 (fancd1) = down cdc23 = down fbxo5 = down h2ax = down haus6 = down mad2l1 = down rab11fip4a = down llgl2 = down ccnb1 = down most tgf betas down

DNA repair genes mcm3,4,6,7 cdc45 hsc70 pcna rbbp4 tert terf1, terf2

Fanconi anemia genes = down


UP _KEYWORDS Cell cycle RT - 135 1.9E-20 5.2E-l8

UP _KEYWORDS Cell division RT - 9 1 1.2E-17 l.7E-l5



GOTERM_BP _DIRECT mitotic nuclear division RT • 63 1.5E-11 2.3E-8


UP _KEYWORDS

GOTERM_BP _DIRECT

GOTERM_BP _DIRECT

D A replication

Gl/5 transition of mitotic cell cycle

D A replication ini iation

ii

ii

i

38

36

19

1.5E-15 9.8E-l4

3. l E-11 3.7E-8

1. 3E-10 l.2E-7

Annotation Cluslllr 3 Enrichment Score: 8.IM k, Cowit . P _ Value BenJ■mlnl

UP _KEYWORDS

UP _KEYWORDS

GOTERM_BP _DIRECT

D Adamaqe

D A repair

D A repair

• • •

67

58

46

4 . 4E-9 l.8E-7

1 .8E-8 5.4E-7

1 .9E-5 5.7E-3

Annotation Cluster• Enrichment Scan: 8.39 Ila. Cowit P _ Yalu■ BenJ■mlnl

UP _KEYWORDS Centromere RT ii 36 1.0E-8 3.6E-7

UP _KEYWORDS Chromosome 8 3.7E-7

GOTERM_BP _DIRECT sister chromatid cohesion 8 6.9E-6

UP _KEYWORDS Kinetochore 7 2.8E-6

GOTERM_CC_DIRECT kinetochore RT ii 20 1.7E-4 9.4E-3

What do these genes do? brca2 (fancd1) = down cdc23 = down fbxo5 = down h2ax = down haus6 = down mad2l1 = down rab11fip4a = down llgl2 = down ccnb1 = down most tgf betas down

mcm3,4,6,7 cdc45 hsc70 pcna rbbp4 tert terf1, terf2

Fanconi anemia genes = down ercc4 msh6 pola1, pola2 prim1

What about duplicated genes?

chromosome behavior genes

Gene baseMean log2FC pvalue padj

camklga 27.345 -2.275 0.003 0.037

camklgb 60.386 1.587 0.010

fabpl0a 5935.662 2.457 0.000

fabpl0b 32.048 -1.766 0.001

fam65a 91.364 1.367 0.002

fam65b 64.561 -1.156 0.009

kcnj2a 97.195 -2.508 0.001

kcn '2b 18.028 ,-.~-Ji .r'_ ~-- --"'."-·- ,. '

. . . .. " "" .' ,;. . ........ . .. " ' ..,._,. ' -

!►....;~. ·_ ' . ._.. -_ -·

Water at North East Cape is toxic to stickleback genome.

What about duplicated genes?

246 TGD gene pairs had at least one copy that was differentially expressed. 21 pairs had both copies differentially expressed.

4 of those 21 pairs had one copy up, other copy down in contaminated fish.


225 TGD pairs had only one copy DE. Study of how they differ with toxicants may give insight into mechanisms.

neofunctionalization subfunctionalization TGD pairs provide that important advantage for analysis of toxicity.

DNA repair pathways: low expression in contaminated sites.

Estrogenic effect on males.

DNA replication: low in contaminated sites. Cell cycle genes: low expression in contaminated sites.

Water at North East Cape is toxic to stickleback genome.

• contaminants persist, • accumulate in fish, • alter endocrine pathways, • alter expression of genome stability genes.

Even after site remediation:

Health of indigenous people is put at risk.




NIH ' DIVISION OF COMPARATIVE MEDICINE

··-·• ~\. Nationa_l Institute of En~ir~nmental Hea~~S · -lilllr'/ Your Environment. Your Health. ciences

Genome duplication and fish models for toxicology Frank von Hippel N AZ U

Loren Buck N AZ U

Tom Titus UO

Pete Batzel UO

Jesse Gologergen Sivuqaq Island

Tiffany Immingen Sivuqaq Island

Ingo Braasch

What are the biological effects?

[vitellogenin] in males (µg/g)

600

400

800

200

0

Suqi River

Tapi River

FUD

Ninespine stickleback

sex genotype PCR

=> estrogenic effect on Suqi males

Sq2 Sq4 Sq5 Sq6 Sq7 Sq11 Sq13 Tapi

What is the genetic response?

: . Mlfouplolo Ind Placental mommolo: 3 homolog1

,-., AHR2. Chicken ENSMGAG00000002128, Turkey

ENSAPLG00000003921 , Duck ENSFALG00000003870, Flycalcher

ENSOANG000000135-48, Pllltypul

Eu1eleol1eomorpha: 42 homolog1

ENSPNAG00000005817, Recl,belllod piranha ENSAMXG00000043051 , Cave fllh

ENSIPUG00000002619, Channel Clttllh ENSPNAG00000015192. Recl,bellled piranha

OOleoglonttonnH: 4 homolog1

EutlleolleOmOrphl: 44 homologa

1hr2, Red-bellied pln1nh1 ahr2, Cove lllh

■hr2. Channel catfish lhr2. Zebrllflah

Teleoat fl111H : 8 homologo ENSPNAG00000003288, Recl,belllod piranha

ahr2, Spotted gar ENSLACG00000018685, Coel1<1nlh

Cheroclphy-: 2 homologl ~ ~--- lhr1a. Zebr1fl1h

lhr11, Northern plkl Oateoglo11tt0nnff: 2 homolog1

lhr1 I. Spotted gar Placental mammala: 14 homotog1

r Homlnlnes: 3 homolog1 AC019117.2, Humon AHR, Hurrn,n f ENSPPYG0000001TT58, orangutan

ENSNLEG00000016550, Gibbon Old World monkeyl: 10 homolog1 New Wor1d monkeys: 4 homologI

0 ENSTSYG00000010830, Tarsler Wet noae lemura: 3 homologa

ENST8EG00000007210, Tree Shrew Rodents: 9 homolog1

Leurul1therl1n m1mma11: HS h0mok>g1 Placental■ : 5 homologa

Marauplala: 3 homok>ga ENSOANG00000009e11 . Ptatypu1

ENSACAG00000023372, Anole lizard e AHR, Chicken

• • , ENSMGAG00000010174, Tur1cey • S ENSAPLG00000008789. Duck L. Perching birds: 2 homologa

ENSPSIG00000010051 , Chlneoe eottohell lurtle ahr, Xenopua

.... ahr1 ■, Coelecanth Lamprey: 3 homologa

ver1e1>r,1eo: 5 homolog1 Perching blrdo : 2 homologo

ENSMGAG00000002118, Tur1cey AHR1B, Chicken

ENSPSIG00000018138, ChlneH aott1hell lurtle r ENSMODG00000027484, Opo11um • ENSOCUG00000028055, Rabbit

Ohr! b, Coelocanth

EuleleOateornO<ph■ : 33 homolog1

lhr1 b, Red-bellied pln1nha lhrl b, Cave fllh

lhr1b, Channel c■ttloh ahr1 b, Zebmllh

• Aatan bonytongue: 2 homolog1

Euleleoateomorphl: 45 homologo

ENSPNAG0000000528 I , Recl,bellled piranha ENSAMXG00000035088, Cava floh

■hr! b, P■romormyropo klng1ieyN ENSLBEG000000111998, B■ ltan wra11e

What does this mean for toxicology? What about AHR?


cytoplasm

nucleus


dioxins AHR

cyp1a1

AHR ARNTAHR

Karchner 2005 Biochem J. 392:153

: . Mlfouplolo Ind Placental mommolo: 3 homolog1

,-., AHR2. Chicken

ENSA~~~~ri.,1!:' Turkey

ENSFALG00000003370, Flye«1.:'1er ENSOANG000000135-48, Pllltypul

Eu1eleol1eomorpha: 42 homologo

ENSPNAG00000005817, Recl,belllod piranha ENSAMXG00000043051 , Cave fllh

ENSIPUG00000002619, Channel cattl1h ENSPNAG00000015192, Recl,bellled piranha

001eoglonttormH: 4 homolog1

EU11leol1e0m0rphl: 44 homologa

1hr2, Red-bellied pln1nh1 ahr2, Cove lllh

■hr2. Channel catfish lhr2. Zebrllflah

Teleoat fl111H : 8 homologo ENSPNAG00000003289, Recl,t,elllod piranha

ahr2, Spotted gar ENSLACG00000018685, Coelacan1h

Cheroclphy-: 2 homologa ~ ~--- lhr1a. Zebr1fl1h

lhr11, Nor1hem pike Oateoglo11ttOrmH: 2 hornololl-'

lhr1 a, Spotted gar Placental mammala: 14 homotog1

r Homlnlnes: 3 homolog1 AC019117.2, Humon AHR, Hu'""n f ENSPPYG0000001TT58, Ofangu1an

ENSNLEG00000018550, Gibbon Old World monkeyl: 10 homolog1 New Wor1d monkeys: 4 homolog1

0 ENSTSYG00000010830, Taroler Wet noae lemura: 3 homologa

ENST8EG00000007210, Tree Shrew Rodents: 9 homolog1

Leurul1therl1n m1mma11: HS h0mok>g1 Placental■ : 5 homologa

Marauplala: 3 homok>ga ENSOANG00000009e11 , PlatypUI

ENSACAG00000023372, Anole lizard e AHR, Chicken

• • , ENSMGAGOOOOOOI0174, Tur1cey • S ENSAPLG00000008789. Duck L. Perching birds: 2 homologa

ENSPSIG00000010051 , Chlneoe eottohell turtle ahr, Xenopua

.... ahr1 ■, Coelecanth Lamprey: 3 homologa

ver1e1>r,1eo: 5 homolog1 Perching blrdo: 2 hornologo

ENSMGAG00000002118, Tur1cey AHR1B, Chicken

ENSPSIG00000018136, C:~!oeH aottahetll tun.Ml r ENSMODG000000274&ii, Opo11um • ENSOCUG0000..'!128055, Rabbit

Ohr1 b, Coelocanth

EuteleOateornorpha: 33 homolog1

lhr1 b, Red-bellied pln1nha lhrl b, Cave fllh

ahr1b, Channel cattloh ahr1 b, Zebralllh

• Aalan bonytongue: 2 homolog1

Euteleoateomorph1: 45 homologo

ENSPNAG0000000528 I , Recl,bellled piranha ENSAMXG00000035088, Cava floh

ahr1 b, Pan1mormyropo klng1ieyN ENSLBEG000000111998, Ballan wraaae



cytoplasm

nucleus


dioxins AHR

cyp1a1

AHR ARNT

zebrafish and chicken have ahr2

zebrafish ahr1a appears to be ortholog of human AHR

zebrafish and chicken have ahr1b

Karchner 2005 Biochem J. 392:153

Documents

Genome Duplication and Fish Models for Toxicology · • Genome duplication in vertebrates zebrafish coelacanth bony fish Two rounds of genome duplication jawed vertebrates gar xenopus