Download Mouse Models Mus Musculus

“The instructions for assembling every organism
on the planet--slugs and sequoias, peacocks and
parasites, whales and wasps--are all specified in DNA
sequences that can be translated into digital
information and stored in a computer for analysis. As
a consequence of this revolution, biology in the 21st
century is rapidly becoming an information science...
...hypotheses will arise as often in silico as in vitro.”
Eric Lander, Science 287 (5459), 1777-1782
Bioinformatics
...TGTTATTGCCAATGCATCATGATCGTAGAGATGTAGGCTAAAGAAACTTTTTTAAAGTGTGATTTTACACAGCAGCTGGTGGTTACTGCTTAGCCATAAAATTATGTGTTGATATTGACATAAGTGGAATGTCGAAAACATGTTTATTCATACACGTATATTGTTG
AAAGAAGTGTTAAACACATCATACGTTTAAAGTAGACAAATCTAGAAATATATAACAAAAGAGAATTTGTTTGTACATTTAAAAAGCCTTAGCTCTTTTTGAGCAAAATATGTAATATTATAATTTCAACACTTTTGAGTGTGTTTACTAAAACTAACAACCTTTAT
GAAGCAATTGGGATGGGTTTGTGTGATCTAAAATTGAGGTAGGATCGTGGGACCAGGAGAACATGAGATGCATCGAAGGCAAAGTCCAAAGACACTACGTCACTTTGAGTGGATTGTGTACGTGAGGTTGTACGAACCATCATTTCACGTTACATATGTTGCAAC
GCTGCGTAATCTGTCCCCACCATCCAACTTATTTCTAATTCTTTTTCATAATTATATTTGTATCTAAACTAAGTAGAATACCTACATATTGAAAAGAAATATTACTTGCTAGGGCCTAGGGATAAACGTTAAAGAGAAATATTACTATAGAGAAAAACCCTTTAGTTT
TGAACACAATTTCTATGTGTAAACATGCGTGATTGTTATGTAGGCAGATGTGCACTAAGCACTTAAACAGAAAAAGAGACAAGTTTTGAACATGAGTTATGAGTAAAACATATAATTATAAAGTTTTGAACATGAGTTATGAGTAAAAACATATCATTATAAAGT
TTTGAGAGCATCTATGAGTAAAAACAGACTAAATTAAATAGAACATATATATGGACAATATAGCAAGTAAAATCTCTCGGACTGACGAAATAGATGTAACTATACTACCAATGCTTGCGATTCAAACCGTCAAAAGTGAAAAATACTGTGAAATAACAAGTCAA
CTTCTATAAATGAAAATTAATATATATTGTAGACGGTTTATATATACGTTTGGATCATATCGATTCACTAATAAAAAAGTAACAAGTGTTATTCCACAAGTTGCATTTTTCATTTGTCTATAAGAACTTTATTGATCTTAAATAACGTTTATGCTTTTTCTTACACATA
TATGGAACCGAATTCAACAAAAACTTTCAAATAGATTTGTTTTATATGAACACAATTATGTATATTGATTGTCCATTTATGAAGAAAAGAATAATCTTATGCTTCACACCGTTGACAAAAAAAGATAAACGTATGTCATTAACCCTCTCTTTTTCTGGTACATGTCA
GAGCAAAGAAAATTTACTAAAAGGTTATTTTGTTTTTCCTTGTTTGTCTATAAATCTACTGAAAGCTTTAAATGCAATTTTATTATTTTCAAGAATCGGTCTTTTTACACTTCCGCGATACTAGCTAAAGGAATGTACACGTGTCAGGATATTATTGTAGCATCTGATT
TTTACCATTGATGGTAACTAAAGTTAGTAACAGAACCATCAGGTCCATCACCGTAAAATATGACTAGCACAGTAGCACCTTTACCAGAAAATAACGCCGTTAGCTGTTTTCATCAAGTCAACAACAACCATTTTAACGGCAGTTTAGATATATTTTAATTTTTTTTA
ACCATATATCATTGGAAGTAAAAAGTTGTCATACTAAAATATATATCTTTTAAGATCTCAAGGTAATTAAAAAAATAATCAAAGACGCTTAAAATCTGAAATTTTCAATAAAGTAATCATAAATTATTTTATGATTTAAATTTAGGTTTATCATAATAATCTTGAAA
GAAATTAAATAATATAATAGTTTTAAGGAAATCTATTTATTTGTTTTTTGATAAATTACATATCTATAGTAAATTAATGATATTGAATGGTGTAGTTGGTTTCTCATAGGTAGAATTAAGACTTTCTCTTTTGTATTAATAAAATTTTATTTGACAACAAACAGAAGA
AACCTTTTAATAAATTGAGAGAGATATACTATAGGACATGATATGACAAAACTGTCCTACTCAGTGAACTTCACTAACAGAGCTCAAATTTGAAATCTCAATGAATTAATATTTAATGACATAACAAGTCAAAGTGATGATATTAAATCTTTCCTCCTTGACAAGA
CGATAATACTTCAATTAACAAAAAAAAAAAAAAAAAGAGATGATAATTTTTCCAGAATAAAATATTTTCGACTTGGACTGGGAATAAAAAAAATGGGGTGACCTAAACCGACGTCGCATAGTTACGAGAGGCATATAAATAGAGAGCCACCAAATAGCCTAAC
GTAGTCCACCTTCACTTGCTCTCTTTTTTCCGAAGAATCTGGTTCGTTTCTCTTTGAATTATCTCTTTCTCTGTTCTTCTTCTTTTTCTAAAGTCTCGAATATATCTTCATTATCATTACTTTATTTGCTTCGTTCTTCCGCAGTTTTGTGCAAAGTTTTAACGATTTTTTGG
TTTTGAACGAAGGCACAGAGAGAAGATGGCGAGTGGCCTCGAGGATATCGTGAACGAGAATGTTGATTTGGTATGGATTTCTTCTTTTTACTCTGTATATATTTTTTTGTTTCGTTTGTTTAACTTGTTTAATGAATATACGAGAGGAAAGTTTAGTTTGGTTTTGTTT
TTTACTTAACGATTCGATCAAATTAGGGTTGTACACAAATCTCGTTACATCATCGTTGAACTATTGACTTCATGTTTTAGCATGAGATTTTTATTGTTTGATTTCGATGAGAAAAGAATCCATGAAAAAGTGTTAATATTATCATAATTATTTCAGTTTTTCTGCTTTTT
TTTCAAAATTACTTTTTCTTTATTTATTTTTTTATTAGATTTTGCAACTGCACTAATTTAAAACAATTTGCAGTCACCAGAAATTTAGTTACAATTATGTAAAAGTTGTTTCCAAATAAAGCAAAAGTAATTACATTAGTAGTACTCTCTACTTTCACATGATCTATCTT
AATGAGTATACTTTGAGATTTCTTAGAGAAGTTTTAGTCAATTCTGTTTTCAATTACTACGTTTTTGGATTTTTCATACTCATGGAATATCGCCTTATCAATCGGTTAATCACTTCCCTAGATAAAACTAAACTTCAATCTTCACCTGATTTTCTGGACTCAATTTAAGA
TACCATGTTATATAGACAGATTTGCCCCTATCAATACATCTTCCGTTACAATGGGCCTTATTGGGCCTTTAGGCTTATTATATAAGCGAATTAAAGTACAAGGCCTTGTGGTCCCACCTTAGATTCTCTGACATCGACAGCTACAGAACATTCCATAATTTTGGTCAT
CTAATATTTTTATGCTTTGATAAATAATTATAATCTTGATTATCTATTAATTTGCATGCTTATATTTTTTTCTTTTTTTTTGCTTTTTTTAGTACTGTAAAAGGTTAACATTTGTATCTGTAAAAAAGATGTACTACAGATAAAAACATACTTGGTTGTTTATTGGTGTAG
GAGATACATAATTATTGAACACCATTTGAATTAGTCTAACATCGTGTTCATATTATATTGCAGGAGAAAATACCTATTGAGGAAGTGTTCCAGCAGTTGAAATGCAGCAGAGAAGGTTTATCTGGAGCAGAAGGAGAAAACAGACTCCAGATCTTTGGCCCCAAC
AAACTCGAGGAGAAGAAGGTATAGTTTGGTTTTAACCATTATCAAAGTCATCATACATGAGCTAAGTCACTAACTATGTAATGGTGGTTTCAATAAATAGGAAAGCAAGTTACTCAAGTTCTTGGGTTTTATGTGGAACCCTCTCTCTTGGGTCATGGAAGCAGCT
GCAATCATGGCTATTGCCTTGGCTAATGGCGGTGGAAAGCCACCGGATTGGCAAGATTTTGTCGGTATCGTTTGTCTTTTGGTTATCAATTCAACTATCAGTTTTGTCGAAGAAAACAATGCTGGAAATGCTGCTGCTGCTCTTATGGCTGGTCTTGCTCCCAAAACT
AAGGTCCCTCTTTATAAACTCCCTTCAAATACTCCTCTTTGCATTAGCATTTACGTGTATGTTTACTGTATACTTGGCATACGAATTACGCGAGTTTAACTATGTTACATAATTAGATTCTTAGCACCTAGTAGTTGTCTAACTTGAAAATGTTTGGCATAAGTAATTG
GTTTACATATAATTTCATTACAAGCTTTTAATAATATTTGTTTTGTTATGACCAGGTTCTAAGAGATGGCAAATGGTCAGAGCAAGAAGCTTCTATTCTTGTTCCTGGAGATATTGTGAGCATCAAGCTTGGTGACATCATTCCTGCTGATGCACGTCTTCTTGAAGG
TGATCCTTTAAAAGTCGACCAATCTGCTTTGACCGGAGAATCTCTTCCCGCAACGAAAGGTCCAGGGGAAGAAGTTTTCTCCGGTTCTACCTGCAAGCAAGGTGAGATTGAAGCGGTTGTGATAGCCACTGGAGTCCATACTTTCTTCGGTAAAGCGGCTCATCTA
GTCGACAGCACAAACCAAGTTGGACATTTCCAGAAAGTTCTTACGGCGATTGGAAACTTCTGCATATGTTCCATAGCTGTTGGTATTGCGATTGAGATCGTTGTCATGTATCCGATCCAGCGCAGACACTACAGAGACGGAATCGACAATCTTCTTGTTCTTTTGAT
TGGTGGTATCCCCATTGCAATGCCTACTGTCTTGTCTGTCACAATGGCTATTGGATCTCACAAGTTGTCTCAACAAGGAGCTATCACAAAACGAATGACCGCCATTGAAGAAATGGCTGGTATGGATGTTCTGTGCAGCGATAAAACCGGGACTCTCACGCTAAAC
AAGCTTAGTGTTGACAAGAATCTTATTGAGGTTTATTGTAAAGGCGTTGAGAAAGATGAAGTTTTGCTTTTTGCTGCTAGAGCTTCAAGAGTTGAGAACCAAGATGCTATTGATGCTGCTATGGTTGGAATGCTCGCTGATCCAAAAGAGGTAATATATATAACTCT
GTTTTTTCCTCTGTTTTAAAATTCTGTTTTTTCCTCTGTTTTGTTTCTTGAAGAAAATGTTCTGTTCTGTTTCTCATTGTTTGTTTCTTTCAGGCAAGAGCTGGAATCAGAGAGATTCACTTCCTACCATTCAATCCAGTTGATAAGCGAACCGCTTTGACGTTTATCGAC
AGCAACGGAAACTGGCACCGAGTAAGCAAAGGAGCTCCCGAGCAGGTAACTAAAACTGATTTTGGTTCTTAAGCTAAGTTAAGTGTTGTGACTTCTTAAAAAAACTGATTCTTTGATGATTTCAGATTCTTGATCTCTGTAACGCGAGAGCTGATCTGAGGAAGAG
AGTCCACTCTACAATCGATAAGTACGCTGAGCGTGGACTTAGGTCATTAGCTGTTTCAAGACAGGTGAGAAGAAATCTTACATTTTGTAACAAGTTATAGGAAGAAGGAAAAAGAGAGAGAGAGTTTAATGTAAATTTTGTGTGTCTATGTTTCAGACTGTACCA
GAGAAAACAAAAGAAAGCTCTGGTAGTCCATGGGAATTTGTTGGTGTGTTGCCTCTGTTTGATCCTCCAAGACATGATAGTGCCGAAACCATTAGAAGAGCTCTAGACCTCGGTGTCAATGTCAAGATGATTACTGGTTTATATCTAAACATTACTCTTCGCTATAG
CGAAAACACCGAATTTCTTACTAATGTTTCCAATGGTTTTATAGGTGATCAACTTGCTATTGCGAAAGAGACAGGACGTAGACTTGGAATGGGATCAAACATGTACCCATCCTCTTCTTTACTCGGTAAACACAAAGACGAAGCCATGGCTCACATTCCTGTTGAG
GATTTGATTGAGAAAGCTGATGGCTTTGCTGGAGTCTTCCCAGGTTTGTTTAAGAGCCATTTTTGTTTCCACAAACACAAACTTGCTCTTCTCTCTGTAACATTTGGTCTCTTTTTTTTCTTTACCAAATTCATTCAGAGCACAAATACGAAATTGTGAAGAAGTTGCA
AGAAAGGAAGCATATCTGTGGTATGACTGGAGATGGAGTGAATGACGCTCCAGCATTGAAGAAAGCGGATATAGGTATCGCTGTGGCGGATGCAACTGACGCTGCACGAGGTGCTTCTGATATTGTCCTCACCGAGCCAGGTCTCAGTGTGATCATCAGCGCGGT
TCTAACCAGTAGAGCCATCTTCCAGAGAATGAAGAACTACACAGTGAGTGTTCTCTTAATCTTAAACCATAACCTTTTTAGAATCTTTACACCATGATAACTTGTTCTCATGGTGTTTTTAAATGTTCCTTTAAACAGATATATGCAGTCTCAATTACCATTCGTATA
GTGGTAAGTAATCAATCTTGTATGTATTCTTGAATATCATCAAATAATCTCTTTTTCTATATGATTTCTCACTTTGTGCCTTTTCACAGTTTGGGTTTATGCTCATTGCTCTAATATGGAAGTTCGACTTTTCACCATTCATGGTTTTGATCATTGCTATATTAAACGATG
GTGAGTTTTTTTCTTCTCTTTAAAAGCTCTCTCTAAATTTTGGCTCTAATCGACTAACACATCATTAACTTACGCAACAGGAACCATCATGACTATCTCAAAGGACAGAGTCAAGCCTTCTCCAACACCAGATAGCTGGAAACTCAAAGAAATCTTCGCAACCGGCG
TTGTTCTTGGAGGCTACATGGCTATAATGACTGTTGTTTTCTTCTGGGCCGCATACAAAACCGATTTCTTCCCGGTATGTAACATATAAACAACCTCTCTTTAGATTCCTTGTCACACAAGCATTAACTTTGTTTGTTTCCTATAGAGAACATTCCACGTGAGAGACTT
GAGAGGCAGTGAACATGAGATGATGTCTGCTTTATACTTACAAGTCAGTATTGTGAGCCAAGCTCTTATATTCGTCACTCGATCTAGAAGCTGGTCTTTTACAGAACGACCTGGATATTTCTTGCTAATTGCTTTCTGGGTAGCACAATTGGTAAGCATTGTATCTTC
TTGATTGATTATAAACTCTCTTGAATGATTGATTCATAAACTTTGACCTTGTAGATTGCAACGGCTATTGCGGTTTACGGTAATTGGGAATTTGCAAGAATCAAAGGAATAGGATGGGGATGGGCTGGAGTAATCTGGCTTTACAGTATTGTCTTCTACTTTCCATTA
GACATAATGAAATTCGCAATCCGTTACATACTAGCCGGAACAGCCTGGAAGAATATCATTGACAACAGGGTACGTTTTGCTTTCTTCTTAGTTCTTCTTCTGAAATGTGATTTTAAGACTTAAACAAAATCTCTCTGTGTCTTTGAAAAAACAGACTGCGTTTACCA
CTAAGCAAAACTATGGAATAGAGGAGAGGGAAGCACAATGGGCTCATGCACAAAGGACTTTACACGGTCTTCAGAACACTGAAACAGCCAACGTTGTCCCGGAGAGAGGTGGTTACAGAGAACTGTCTGAGATTGCAAATCAAGCCAAGAGACGAGCTGAGAT
CGCAAGGTAAATGATTTGTAAAAAGTAATTTCGGTTTCTTGTGAGAGAAGTTAACGTTAGGGTTTTTGTTTACAGGCTTAGGGAACTTCATACGCTTAAAGGACATGTAGAGTCAGTGGTGAAGCTAAAGGGACTAGACATTGAGACAGCTGGTCACTACACCGTT
TAATAAAGATTTAACAAGAAGATGATTAAGGAAGAAGAAGATCCTTTTGTTTAAGAGATGATAATGATGATGATTTTATAACAAGAGAATAAGGTTTTTTTTCTGTGTATGTTAAGTTCCTCTAAACTCCTGGGGTTTTTCTTCCTTCCTTATTCATGGTTTTAGACT
TTAATTATAACCATGTGTTTTTGTTTCCCCTCTCTTGAATAAAAAAGAGAAGATACTAATATCATAGGTTTAATACGTTTATGTTTTATAAAAGTTCAATAGATATTGTTTTTGGATATTATGTGAACATAACAATATTTATAAATTCACCTTTCAATTTTCTTATGAG
ATGATATCATCTTTACTACTTAAAATATCTTCTAATTAAACCAAAAGCAGATTTAGGTCCGGTTAGATGAATAACCGGTTCGATTAATTTCGTCAGACCGATTTGATCCGTGGATATCATTAATCCGTGGAATACATGTGTGTTCTTGAGTAGGCCACTAGTTATAAT
CCACGTGGCAAGCATTTTATCACAAACCCAGAGCTACAAAAACAAAACCAAGAAGACGAGAAGGATCTTTAACAGAGAAAAAAGAGCTTTAGACCAAATCACCAGAAACAAAACAAAAATGTATTTCGCCGCCATAGCTTCTTCACGACAAAGCTTTTTGTCAA
ACAATTTCAGTTTCCAACACAGTTTTAAACCCAAATCCAATGTTAACCTCACTCGTCCTAATTCAATCTGTTGTAAATCTTCACACCACGACGACGAAACTGATTCTTCTCGGTAATTTTTATTTACCTTTAGAAAATTTTTTTCCGATTCTAAACTCGGGTTTGGTCTT
ATTCAATCTTTTATTTATCTATTGATTAGGAAAAATGAAAATCAGCTGGCGAAGTTGGCAATCGCGACGCTAGCGGTTGGCGTTTTGGCTTATTAAGGAAGAAGAAGATCCTTTTGTTTAAGAGATGATAATGATGATGATTTTATAACAAGAGAATAAGGTTTTTT
TTCTGTGTATGTTAAGTTCCTCTAAACTCCTGGGGTTTTTCTTCCTTCCTTATTCATGGTTTTAGACTTTAATTATAACCATGTGTTTTTGTTTCCCCTCTCTTGAATAAAAAAGAGAAGATACTAATATCATAGGTTTAATACGTTTATGTTTTATAAAAGTTCAATAG
ATATTGTTTTTGGATATTATGTGAACATAACAATATTTATAAATTCACCTTTCAATTTTCTTATGAGATGATATCATCTTTACTACTTAAAATATCTTCTAATTAAACCAAAAGCAGATTTAGGTCCGGTTAGATGAATAACCGGTTCGATTAATTTCGTCAGACCGAT
TTGATCCGTGGATATCATTAATCCGTGGAATACATGTGTGTTCTTGAGTAGGCCACTAGTTATAATCCACGTGGCAAGCATTTTATCACAAACCCAGAGCTACAAAAACAAAACCAAGAAGACGAGAAGGATCTTTAACAGAGAAAAAAGAGCTTTAGACCAAAT
CACCAGAAACAAAACAAAAATGTATTTCGCCGCCATAGCTTCTTCACGACAAAGCTTTTTGTCAAACAATTTCAGTTTCCAACACAGTTTTAAACCCAAATCCAATGTTAACCTCACTCGTCCTAATTCAATCTGTTGTAAATCTTCACACCACGACGACGAAACTG
ATTCTTCTCGGTAATTTTTATTTACCTTTAGAAAATTTTTTTCCGATTCTAAACTCGGGTTTGGTCTTATTCAATCTTTTATTTATCTATTGATTAGGAAAAATGAAAATCAGCTGGCGAAGTTGGCAATCGCGACGCTAGCGGTTGGCGTTTTGGCTTTGGGAAGTGT
TGGGGATGCGTTTGCGGCCAAAAGCGGTGGAAGAATCGGCGGTCAAGCGTTTCGGTCTTCAGCTCCTCGTCCTCCTCCCAGAATTAACAATCGATCAAGGTAAAATTTTTTACTTGAAGCTCTAATCTCGATTTTAATTATTTAATATGTATATGATTAAAATACTG
GCGAAAAAAGTATATATTTAAATTAAGACCTTAATTGAGATTTCTTACAAGAGACTCCATGTATGGGCTTTTAGCAGCCTCATATCCACATTAAAGCCCATTAGTAAACTTTAAGCCTCTTATAATTTTCTATTACACTTTATATTTTGAACCCCATAATTACAATTC
GAATCCAAGATACCCCAACGACCAACACTAATAACTTGATTCAATGCATTAGGCTTTTCTGTTTGCATTATATAATCACGACTTTAGTCTTAGTAGTTAGTACCTTTGCATTCTAAACGCAGCTTTGTTTTCGCAGGACCAACATCTACGTGAATCCTCAGGTTGCAC
CACCTTTGATCGGTGGCTATGGATATGGTTACGGAGGTTACGGATGGTCACCGTTTTCCTTTTTTGCCCCTGGTCCTGCGGTGGCAGTAGGTGTTGGCGGTGGCTTTGACCTCCTACTTCTCTTCATGTTTTTTGGAGCCGCTTCAGCCGTCGCTAGAAACTTTTTCCG
ATCAAGAAATGATGAAGATGACGAAGACGACTATTAGAGGAGAAAACGGAGAGAGGCTTATGTAACAATAGTCATACATACGATTTTGTGTAAAAAAATATGATGGAAGAAGACGGATATATGTGGAAATCTTGAAATAAGTAACTAAAGACCCATCTTAAAG
TTAATAGAGGCAATTTGAAAACACCTCCAAATACTAAATTTATATACAAATTTTCTCTGTTTTTCCTTCATTCTTTATATTTTAGGTTCTAGTGTATGACCTCATTGGTCTCCGAAAGCAAGTGAAAATAAATTCTTTAAGCAACCAAATATAAAGAAAACATTGGTA
TATTTTGTCAATGGTTTATCAGTGTTAACGAAGAAGAATAATTAGACCTAGCTAAAAGTGAAATCAGTAAATCTCGTAAATAATAATAACGATAAATCAGATACAAAAAGAAAATAAAAAAATCAAGAAGAAGACGAAGAAGAAAAAAGAAAGAGTCAGTGAA
TTAACAAAAATCAAGAAGAGGTTCGGTTAATACTAAGTCCTTGAAAGAGCCAATGAGGTCTCTTCTTCTCTCGATCCAACGACGTCGTACTTGAGCTGCTCATAGGCGTGTTTGGTCCGCTACTTTCTTGGTTATTATTGCTGTTATTATATAGATTATTATTGCTCT
GATTATTACAATTATCCGATGATGAT...
Functional Genomics
The analysis of the DNA sequence of genes and
genomic regions reveals evolutionary
relationships, and can be used to (amongst a
gazillion other things), to...
– assign function to DNA that codes for peptides,
• at the physiological level (i.e medical in Humans),
• at the protein structure level.
The Problem(s)
Big Problem: Cardiovascular Disease: 40.1% of deaths in 1999 (USA)
Genomic Challenges
besides being huge
…recognizing genes in the genome,
•
•
•
Exons/Introns,
Alternative Splicing/Termination,
…determining the function of
the gene,
•
no known homologies,
•
gene families,
•
etc.
Alternate transcription start/stop sites,
•
Tandem Repeats, Psuedogenes, etc.
•
We don’t really understand all there is to know
about gene structure,
•
etc.
Nature: 407, pp. 234
Cardiovascular Disease
Lipids
…major players in heart disease.
Cholesterol,
Triglycerides,
•
•
most common fat in the body, energy
storage molecule,
•
found in fat cells, blood plasma, and cell
membranes,
•
derived from eaten fats or made from
other energy sources.
•
a steroid alcohol (sterol) used to
insulate nerves, produce human sex
hormones and as a component in cell
membranes,
produced by the body and supplied by
diet.
Lipoproteins
…and classes.
Apolipoprotein Gene Family A
(APOA)
Low Density Lipoprotein
LDL
Associated with HDL,
Removes cholesterol from the blood,
Modulates trigyceride levels.
Chromosome 11
(H.s.)
•
•
Several apolipoproteins map to a region of chromosome 11, including two APOA genes,
There is a polymorphism that is linked with high serum triglyceride levels that maps to the same
region.
Hypertriglyceridemia
Why bad?
…high levels have been linked with coronary artery disease,
Normal
Borderline
High
Very High
<150 mg/dL
150-199 mg/dL
200-500 mg/dL
>500 mg/dL
American Health Association Recommendation
Changes in lifestyle habits are the main therapy for hypertriglyceridemia…
•If you're overweight, cut down on calories to reach your ideal body weight.
•Reduce the saturated fat and cholesterol content of your diet.
•Reduce your intake of alcohol considerably.
•Be physically active for at least 30 minutes on most days each week.
•Substitute monounsaturated and polyunsaturated fats
•Substitute fish high in omega-3 fatty acids instead of meats that are high in saturated fat.
A Solution
…to finding genes.
Mouse Genome:
~ 2.75 Gb,
19 autosomes + X and Y
chromosomes,
99% per cent of the mouse genes
have a sequence match in the
human genome,
96% lie within 'syntenic' regions of
mouse and human chromosomes.
Nature 420, 515 - 516
Mus Musculus
Conserved Synteny
Description of DNA segments in which gene order is identical between species.
The Solution
% similarity between
M.m. and H.s.
Comparative Genomics
High homology, no annotation.
How did they know the region was expressed?
- not including the Northerns.
New Gene Structure?
Mouse: 1107 Open Reading Frame (ORF), 368 AA,
Human: similar structure, 366 AA,
Most similar to each other (71% identity, 78% similarity),
Next most similar to APOAIV (27%, 48%)
movie
The Solution
…to determining function (I, II).
Mech Dev. 76(1-2)
I. Transgenic Mice:
- DNA is integrated in a random fashion
by injecting it into the pronucleus of a
fertilized ovum,
wt
II. Knock-Out Mice:
- DNA is introduced first into embryonic
stem (ES) cells. ES cells that have
undergone homologous recombination are
identified and injected into a 4 day old mouse
embryo - a blastocyst.
GFP
PNAS 97
Glutamic Acid Decarboxylase 67
Pronucleus: either of the 2
haploid gamete nuclei just prior
to their fusion in the fertilized
ovum.
Transgenic Mice
Pronuclear Injection
1, heart; 2, brain; 3, placenta; 4, lung;
5, liver;
6, skeletal muscle; 7, kidney; or 8, pancreas.
WT Mouse mRNA
hybridized with mouse
APOAV cDNA
WT Human mRNA
hybridized with human
APOAV cDNA
1 and 5, transgenic liver;
2 and 6, transgenic intestine;
3 and 7, wild-type liver;
and 4 and 8, wild-type intestine.
H.s. APOAV probe
Fig. 2
APOAV Transgenic Mice
“overexpressors”
n=48 (transgenics), n=46 (controls), P < 0.0001
Typical KO vector
…and homologous recombination.
KO
transgenic
*tk:thymidine kinase + gancyclovir = lethal
KO Mice
w/ Embryonic Stem Cells
Transformed ES cells are injected
into blastocysts
Chimeric mouse
Black/White Chimeric Example
Cross and look for
offspring with germ-line
transfection.
Ref. 25
Expression of native APOA mRNA.
Fig. 2
APOAV KO Mice
“underexpressors”
n=13 (wt), n=22 (hets), n = 10 (homozygous mut.) P < 0.001
Fig. 3
Murine Models are Good
…but what about us?
• Identified 4 SNPs in and near the human APOAV locus
(each occurs at >8%),
• Surveyed ~500 Caucasians for numerous lipid
parameters before and after high- and low-fat diets,
Fig. 1A
1,1 = homozygous for major allele
1,2 = heterozygous for major allele
•
Individuals heterozygous for the minor alleles at SNPs 1-3 had significantly higher
triglyceride levels and VLDL mass.
•
SNP4 does not show a significant difference in triglyceride levels or VLDL mass.
Linkage disequilibrium: When the observed frequencies of
haplotypes in a population does not agree with haplotype frequencies
predicted by multiplying together the frequency of individual genetic
markers in each haplotype,
English Translation: The co-occurrence of genetic markers more
often than would be expected.
SNP1, SNP2, & SNP3 have significant disequilibrium with each other
while SNP4 is not in linkage disequilibrium with any other SNP,
English Translation: this genetic region containing SNP1-3
segregates as a “unit”.
Independent Association Study
Data from an independent set of individuals demonstrating that subjects with
minor alleles at SNP3 are significantly more likely to have high triglyceride
levels than low.
Summary
• Comparative Genomics
uncovered a new gene in
the human genome.
• Mouse transgenic and KO
experiments suggest that
the protein contributes to
triglyceride and VLDL
levels.
• SNP data shows that APOAV
plays a significant role in plasma
triglyceride and VLDL
homeostasis.
• Polymorphisms of APOAV
could be used as prognostic
indicators for
hypertriglyceridemia.
• Modulation of APOAV is a
potential strategy for reducing
risk of cardiovascular disease.
APOAV Update
http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=apoav
Weds.
~Genome scale KO experiment.