The Amazingly Similar Genes of Dogs, Humans, and Mice

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The Amazingly Similar Genes of Dogs, Humans, and
Mice

• Andrew G. Clark and Stacey L. Hubbell
• Institute of Molecular Evolutionary Genetics
• Department of Biology
• Penn State University

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Motivation for dog genomic analysis

• Our acute awareness of dog phenotypes.
• Model for cardiac physiology.
• Depth of knowledge of nutrition.
• Genetic partitioning by breeds.
• Extensive documentation of behavioral,
  phenotypic, and morphological variation among
  breeds.
• Human and dog chromosome maps line up well.
• DNA sequence similarity to human.

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Wide diversity of forms of the domestic dog
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Human Diseases with Dog Equivalents(selections
from a list of more than 350)

• Milroys disease
• Endocardial fibroelastosis
• Congestive heart failure
• Hyperadrenocorticism
• Hyperinsulinism
• Achalasia
• Ulcerative colitis
• Pacreatitis
• Hepatorenal syndrome
• Von Gierkes syndrome
• Cyclic neutropenia
• Multiple myeloma
• Hemophilia
• Factor VII deficiency
• Christmas disease

• Globoid leukodystrophy
• Familial amaurotic idiocy
• Neurogenic muscular cramps
• Hypoplasia of organ of Corti
• Retinal dysplasia
• Diabetic microaneurysms
• Prostatitis
• Hechts pneumonia
• Osteogenesis imperfecti
• Disk luxation
• Acetabular dysplasia
• Ehlers-Danlos disease
• Seborrheic dermatitis
• Impetigo
• Uremia

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Gray Wolf Canis lupus lycaon
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Sequences of mitochondrial DNA show that dogs
and wolves have often interbred.
Vila et al. 1997. Science 2761687-1689.
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A wolf-dog hybrid owner says
"I have two wolf-dogs I take everywhere. I never
fail to hear how they are the best-behaved
animals ever seen. My dogs come when they are
called. They also sit, stay and heel as well,
with or without a leash. They both get along well
with neighbors' ducks, geese, goats and horses. I
throw large summer parties and my hybrids mingle
among the guests and their children.
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The power of mouse genetics

• Rich history as a model organism
• Huge knowledge base of human- mouse gene
  matches.
• Complex disorders diabetes, hypertension,
  obesity
• 6992 mapped protein genes
• 7377 mapped microsatellites
• Gene knockout technology

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Human Diseases with Mouse Equivalents

• Hypertension
• Thyrotropin deficiency
• Obesity
• Megacolon
• Niemann-Pick disease tumors
• Macrocytic anemia
• Prenatal muscle degeneration
• Dystrophy of white matter

• Cochlear degeneration
• Pigmented retina
• Uterine cystic hyperplasia
• Lung tumors
• Senile osteoporosis
• Clubfoot
• Albinism
• Diabetes insipidus
• Renal amyloidosis

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Homology similar form due to common ancestry
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Phylogenetic relationships
Homo sapiens
Canis lupus familiaris
Mus musculus

• Molecular Clock Estimates
• Human-dog split 83 MYA
• Human-mouse split 112 MYA

(Kumar and Hedges 1998 Nature 392917-920) (OBrie
n et al. 1999 Science 286458-481)
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Our study plan

• Retrieve all complete dog gene sequences (n
  254).
• Find human and mouse homologous genes with BLAST.
• Align the dog-human-mouse sequences.
• Calculate sequence divergence and interpret the
  meaning quantitatively.

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blast_tmp 241 ttgccaagccctgtcggagatgatccagtttta
cttggaggaggtgatgccccgggctga 300 dog U39569
237 ..........t....c.................t.........
..........a...... 296 U38200 237
..........t.......................c...............
...a...... 296 AF060520 237
..........t....c.................t................
...a...... 296 L26029 244
..........t....t..................c...............
...aa..... 303 AB000514 237
..........t....t..................c...............
...aa..... 296 L26031 244
..........t....t..................c...............
...aa..... 303 L26030 244
..........t....t..................c...............
...aa..... 303 M57627 267
..........t....t..................c...............
...aa..... 326 human U11767 240
..........t.......a...............c...............
.a.a...... 299 AF043333 183
..........t....t..................c...............
...aa..... 242 U11421 255
..........t.......a...............c...............
.a.a...... 314 Z29362 308
..........t.......a...............c...............
.a.a...... 367 U00799 237
..........t.......a...............c....a..........
.a.a...... 296 AF088887 237
a.........t.......................c..a....c.......
.g.aa..... 296 AF068058 283
a.........t.......................c..a....c.......
.g.aa..... 342 AF012909 303
..........t.......................c.a.t...........
...a...a.. 362 U93260 293
..........t.......................c.a.............
.gaa...... 352 L37781 305
..........t.a..a..a...............c...ta..a.......
...a...a.. 364 NM_010548 312
..........t.a.....a...............c...ta..a.......
...a...a.. 371 mouse L02926 238
..........t....a..a......a........c...ta..a.......
...a...a.. 297 NM_012854 281
..........t....a..a......a........c...ta..a.......
...a...a.. 340 X60675 281
..........t....a..a......a........c...ta..a.......
...a...a.. 340 AF097510 302
............a.....a...............c...ta..a.......
...a...a.. 361 AF054604 129
......t...t....c.................t................
...a...... 188
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Non-automatable aspects

• Checking gene families
• Gene redundancies
• Sequencing errors
• Files containing introns
• Mitochondrial DNA

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The Central Dogma DNA makes RNA makes protein.
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Coding amino acids from RNA
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The Genetic Code
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Some definitions

• Silent site a letter in the DNA code that can be
  changed without changing the protein encoded by
  the gene (also called synonymous)
• ps proportion of silent sites that have changed

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• Mis-sense mutation an altered letter in the DNA
  code that changes the amino acid sequence of the
  protein encoded by the gene (also called
  nonsynonymous).
• pn proportion of mis-sense sites that have
  changed.

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Most genes show much higher levels of silent
divergence
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Ratios of mis-sense to silent rates
r 0.933
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Genes with excess mis-sense divergence

• IDUA - a-L-iduronidase
• CLN2 - pepstatin-insensitive lysosomal protease
• NOS - nitric oxide synthase
• CD34 - hematopoietic progenitor cell marker
• PTH1 - parathyroid hormone receptor-1
• MMAC1 - mutated in multiple advanced cancers
• GHR - growth hormone receptor

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Inferred locations of substitutions on the tree
dog
7902
14448
mouse
7062
human
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Relative rates tests for silent and mis-sense
sites
Growth hormone receptor
silent mis-sense dog 40 16 hum
an 27 43 X2 13.49
Translation GH receptor gene is evolving way too
fast in humans !
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Unusually highly conserved genes tend to code for
very basal functions
GAq GTP-binding protein alpha 2 0.000000 rab2 GT
P-binding protein (rab2) 0.000000 SPC22 microsoma
l signal peptidase 0.000000 SPC18 microsomal
signal peptidase 0.000000 Sec61-B protein
translocation complex 0.000000 tektin tektin
(sperm development) 0.000000 centractin centractin
(microtubule org.) 0.001379 rab7 GTP-binding
protein (rab7) 0.002494 mitogen mitogen
activated protein kinase 0.002920 ubiquitin ubiqui
tin-tagged degradation 0.004032 Kv3.1 Kv3.1
potassium channel 0.005252 fosB fosB
transcription factor 0.006070
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The X chromosome of humans and cats has the same
gene order!!
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Conclusions

• Almost all human genes can be lined up
  unmistakably to genes in dogs, with an average
  mis-sense divergence of 7.5.
• By having three species with aligned genes, we
  can do branch-specific inferences.
• The lineage to dog has faster silent rate
  relative to the lineage to humans
• but the human branch has an elevated mis-sense
  rate.
• Several genes with elevated mis-sense rates
  suggest that evolution is driving these genes
  along at a faster rate than others.

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Some dog websites

• www.rufruf.com
• www.purina.com
• www.pfizer.com
• www.petnet.com
• www.petwellness.com/doghome.asp

www.vgl.ucdavis.edu/research/canine/ www4.ncbi.nl
m.nih.gov/PubMed/