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Genomics
MUPGRET Weekend Workshop
Timeline Answers
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http://www.jgi.doe.gov/education/timeli
ne_2.html
Another timeline at
http://www.dnai.org/index.htm .
Reviewing the basics
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Cells are the basic working unit of an
organism.
DNA (deoxyribonucleic acid) contains all
of the instruction needed to direct the
activities in the cell.
DNA is arranged into chromosomes.
More reviewing
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Chromosomes are visible with high
powered microscopes.
Chromosomes are Dynamic Structures
Human Chromosomes
CONDENSED
EXTENDED
Metaphase
Chromosome
Fruit Fly
More review
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Chromosomes contain hundreds of
genes encoded within their DNA.
Genes compromise a very small
percentage of the DNA that makes up
the chromosome, <5% generally.
DNA containing genes is called
euchromatin.
Heterochromatin
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Non-genic DNA is called
heterochromatin.
Heterochromatin and euchromatin stain
differently.
This difference causes the bands we
see in a karyotype.
Human karyotype
Genome composition
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Euchromatin (genes) usually contains a
higher proportion of GC.
Euchromatin has more unique DNA
sequences.
Heterochromatin (non-coding) usually
contains a higher proportion of AT.
Heterochromatin contains more
repetitive sequence.s
DNA Content
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The amount of heterochromatin varies
dramatically between organisms.
Much of the difference in DNA content among
closely related organisms is often due to
changes in heterochromatin amount.
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Maize 2500 Mb
Wheat 16,000 Mb
Rice 430 Mb
Mb=Mega base pairs
A NOVA look into DNA.
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http://www.pbs.org/wgbh/nova/photo5
1/jour-nf.html
PCR
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Polymerase Chain Reaction
A way to “xerox” a DNA fragment.
Electrophoresis
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A way to separate DNA molecules.
http://gslc.genetics.utah.edu/units/biot
ech/gel/
What is genomics?
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The study of the entire DNA
complement of an individual.
The term genome refers to all of the
DNA contained in one copy of the
chromosomes of an organism.
It contains both coding (genes) and
non-coding DNA sequences.
The Genome
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Nearly every cell in an organims
contains a full copy of the genome.
Most mammal cells contain two
complete copies of the genome.
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Skin
Lung
Heart
The Genome II
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Gametic cells like sperm, ovules, or
pollen contain one copy of the genome.
Some special cell types contain more
than two copies of the genome.
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Human bone marrow
Regenerating liver cells
Plant Genome
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Corn plants contain two copies of the
genome in their cells except for pollen,
ovules, and endosperm (the fleshy part
of the corn kernel).
Pollen and ovules have one copy of the
genome.
Endosperm has three copies.
Plant Genome
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Other plants like corn include:
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Arabidopsis
Barley
Beans
Tomato
Pepper
Rice
Multicopy Plant Genomes
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Some plants normally have more than
two copies of the genome in their cells.
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Wheat – six copies
Potato – four copies
Sugarcane – >twelve copies
Strawberry – >eight copies
Banana – three copies
Watermelon – three copies
Chromosome number
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The term haploid refers to the base
number of chromosomes in an
organism.
Diploid cells have two copies of all the
chromosomes.
How Many Chromosomes Are There?
Bacteria usually have one circular
chromosome and no nucleus
Organisms with nuclei have
variable numbers of chromosomes
depending on the species:
• Mosquito 6
• Chimpanzees 48
• Goldfish 94
How Many Chromosomes Are There?
Some plants have few
chromosomes like Arabidopsis.
Others, like sugarcane, have many.
Wheat
42
Rice
24
Arabidopsis
10
Sugarcane
+100
Maize
20
Potato
48
Tomato
24
Cabbage
20
Carrot
18
Ploidy vs. chromosome number
Organism
Ploidy
Corn
Diploid (2X)
Chromosome
number
20
Tomato
Diploid (2X)
24
Arabidopsis
Diploid (2X)
10
Potato
Tetraploid (4X)
48
Wheat
Hexaploid (6X)
42
How many genes?
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The number of genes varies between
organisms.
Humans – 30,000 to 40,000
Maize – 55,000
Most genes between closely related
species are conserved.
Many genes between less closely
related species are conserved.
The human genome project
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Complete DNA sequence
Understand the sequence variation
between individuals.
Understand the function of genes.
Compare the sequences to other related
organisms.
Study the ethical, legal and social
implications.
The human genome project
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http://www.genome.gov/Pages/Educati
onKit/download.html
Exploring our molecular selves video.
Ethical legal and social implications
video.
Insight from the human genome
draft sequence
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Protein coding region <2%.
Repetitive DNA minimum of 50%.
Genes are randomly distributed.
3X as many proteins as Drosophila or C.
elegans because of post-transcriptional
modifications.
Insight from the human genome
draft sequence II
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Humans, C. elegans, Drosophila, and
plants have most of the same proteins.
There are 2X as many germline
mutations in males vs. females.
DNA sequence between two individuals
is almost identical.
Only 0.1% of sequence is different.
Where do we go from here?
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Gene Expression
Proteomics
Structural genomics
Mutagenesis
Comparative genomics
Medicine and the New Genomics
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Gene Testing
Gene Therapy
Pharmacogenomics
Anticipated Benefits
•improved diagnosis of disease
•earlier detection of genetic predispositions to disease
•rational drug design
•gene therapy and control systems for drugs
•personalized, custom drugs
Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Medicine and Society: A 2001 Primer, 2001
Ethical Considerations
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Privacy/confidentiality
Reproductive issues
Accuracy of genetic testing
Access to technology
Genetically modified foods and
microbes
Commercialization/Patents
Benefits of Genomics
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Improved diagnostic tools.
Rational drug design.
Rapid identification of pathogens.
Better understanding of mutagenesis.
DNA forensics
Improved agricultural products
Plant Genome Projects
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Initiative began in 1998.
Arabidopsis was the first model plant.
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Small genome size.
Little repetitive DNA.
Short life cycle.
Arabidopsis 2010 Project
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Complete sequence of Arabidopsis in
2000.
2010 Project started in 2001.
Goal was to determine the function of
the 25,000 genes in Arabidopsis by the
year 2010 (ie. functional genomics of
Arabidopsis).
Tools for genomics
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Sequencing video from human genome
project.
Downloadable from
http://www.genome.gov/Pages/Hyperio
n/educationkit/download.html