Download 37_Genomes

Lecture Outline 12/7/05
• The human genome
– Most of our DNA is non-coding
• Various types of repetitive elements
– Gene families
• Some applications of genetic
technologies
• Future of genomics?
• Course Review
On February 11, 2001, two
groups published the sequence
of the entire human genome
But that doesn’t mean we can read it . . .
Overview of the human genome
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Exons (regions of genes coding
for protein, rRNA, tRNA) (1.5%)
Introns and
regulatory
sequences
(24%)
Unique
noncoding
DNA (15%)
Alu elements
(10%)
Simple sequence
DNA (3%)
Large-segment
duplications (5–6%)
Repetitive
DNA
unrelated to
transposable
elements
(about 15%)
Numbers and types of genes in
different eukaryotes
Most genes have
uknown function
Areas of high and low gene density
Movement of eukaryotic transposable
elements
Transposon
DNA of genome
Transposon
is copied
New copy of
transposon
Insertion
Mobile transposon
(a) Transposon movement (“copy-and-paste” mechanism)
New copy of
Retrotransposon
retrotransposon
DNA of genome
RNA
Reverse
transcriptase
Insertion
(b) Retrotransposon movement
Figure 19.16
Many genes
occur in gene
families
DNA
RNA transcripts
Non-transcribed
spacer
Transcription unit
DNA
18S
28S
5.8S
rRNA
Ribosomal RNA
genes
5.8S
28S
18S
(a) Part of the ribosomal RNA gene family
-Globin
Heme
Hemoglobin
-Globin
Globin genes
-Globin gene family
-Globin gene family
Chromosome 16
Chromosome 11

Figure 19.17
Embryo
 
2

1
2
1 
Fetus
and adult

Embryo
G
A
Fetus



Adult
(b) The human -globin and -globin gene families
Histone gene distribution
Gene duplication due to unequal
crossing over
Transposable
element
Gene
Nonsister
chromatids
Crossover
Incorrect pairing
of two homologues
during meiosis
and
Figure 19.18
Evolution of the human -globin and
-globin gene families
Ancestral globin gene
Duplication of
ancestral gene
Mutation in
both copies


Transposition to
different chromosomes


Further duplications
and mutations


Figure 19.19

  

2 1 
-Globin gene family
on chromosome 16
2
1



G

A

 -Globin gene family
on chromosome 11


Evolution of a new gene by exon shuffling
EGF
EGF
EGF
EGF
Epidermal growth
factor gene with multiple
EGF exons (green)
Exon
shuffling
F
F
F
Fibronectin gene with multiple
“finger” exons (orange)
Exon
duplication
F
F
EGF
K
K
Plasminogen gene with a
“kringle” exon (blue)
Portions of ancestral genes
Figure 19.20
Exon
shuffling
TPA gene as it exists today
K
Some other uses of genetic
technology
Replacement of Neanderthals
by Modern Humans
Generations before present
Currat and Excoffier 2004
Ovchinnikov et al 2000 Nature 404:490-493
Poaching Whales?
Data from Baker and Palumbi 1990
www.okstate.edu/artsci/zoology/ravdb/Cons.%20Genet...
Minke whale
Minke whale
Sample #19a
Sample WS3
Sample #9
Sample #15
Sample #29
Sample #30
Sample #36
Sample #6
Minke whale
Sample #18
Sample #19b
Humpback whale
Humpback whale
Gray whale
Gray whale
Blue whale
Blue whale
Sample #41
Sample #3
Sample #11
Sample WS4
Fin whale
Fin whale
Sei whale
Sei whale
Bryde’s whale
Bowhead whale
Bowhead whale
Right whale
Pygmy right whale
Sperm whale
Pygmy sperm whale
Sample #16
Harbor porpoise
Sample #13
Sample #28
Hector’s dolphin
Commerson’s dolphin
Killer whale
Particularly variable regions of DNA can be
used as “genetic fingerprints”
• Can any of these
children be excluded
from being the
biological child of the
father?
Mother
Father
The future?
• Patterns of expression?
• Regulatory networks?
– Gene-> phenotype
• Patterns of variation?
• What is all the non-coding DNA?
Patterns of Gene Expression
• “Gene Chips” or
microarrays can
compare expression
levels of 1000s of
genes at once
Understanding Variation