Transcript Genomics - West High School

Genomics
The field of biology based on studying the entire DNA
sequence of an organism - its “genome”.
Genomics tools don’t replace classical genetics tools,
they are complementary.
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Classical Genetics (forward genetics):
1. Mutant studies
A. Find mutants and reproduce them
•Natural mutations
•Create mutations by using mutagens
(selective pressure for mutants to
survive)
example: antibiotic resistant bacteria
B. Study genes one at a time
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What makes Genomics a new
way to study biology?
Genomics: Using tools to study all the genes in an
organism (the entire genome) simultaneously once its
sequence is known. (~ 190 organisms as of March
2007)
How do we do this?
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Genomics methods
Be Efficient:
1. Work with Model Organisms Share resources and information
E. coli (Bacterium)
Arabidopsis (Plant)
ZebraFish
Dictyostelium (Slime mold)
Xenopus (African clawed frog)
Drosophila (Fruit Fly)
Mouse
S. cerevisiae (Yeast)
C.elegans (Worm)
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Genomics methods cont’d
2. Use Reverse Genetics:
A. Insert tagged DNA sequences (T-DNA) at
random sites throughout the genome. If the
insertion disrupts a gene, then it might
cause an observable phenotype.
B. Grow the organism.
C. Look for mutant phenotypes.
.…Since the insertion has a specific sequence (a
tag), you can figure out where the insertion went
in the genome =>then you figure that gene is
related to that phenotype. Voilà!
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Genomics Methods, Cont’d
3. Use High through-put
methods that produce huge
datasets
==> One method is a Microarray
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Microarrays (slang: DNA chips)
Ordered array of different known sequences
of DNA (~20-70 bp)
on a solid surface (glass)
Can have thousands of “spots”. This slide has 18
Gene 1
Gene 18
Gene 2
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“DNA Chip”
Slang for DNA Microarray
=>Technology using a biological
molecule:
DNA
A
G
T
C
•many different DNA sequences stuck to
a flat surface
•tens of thousands of spots
•can probe tens of thousands of DNA
sequences all at once
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How do Microarrays work?
In general:
1. Cells express certain genes under certain conditions
and make RNA
2. RNA is isolated and tagged with a dye
3. Tagged RNA is placed on a microarray containing
representative sequences of thousands of genes
at known addresses on the chip
4. Microarray is scanned to locate where dye is
=> this is where RNA has attached
=> voila! these genes were expressed
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“Alien “ oligos
be spiked
Labeled
Targetcan
DNA
made
onto the array spots as well as
from RNA present in cells (a
into the treatment+reference
“snapshot” of gene
mix in known concentrations.
expression)
Hybridized target
to Probe DNA
Probe DNA stuck to glass
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Temple Smith, Boston U