Download Explain the difference between the following types of genome maps

Objective # 16
Module 4C – Genomics
Explain the difference between the
following types of genome maps,
and explain how each type of map
i constructed:
is
d
a) genetic maps
b)physical
b)
physical maps
The complete set of genetic instructions
for an organism is referred to as its
genome.. In this module, we will
ggenome
examine genomics – the science of
mapping and studying entire genomes.
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Objective 16
Objective 16
 Genome
maps are used to determine the
location of genes. Maps of genomes are
constructed at different levels of
resolution using different kinds of
information.
 Depending on the type of map we use, a
gene can be located on a particular
chromosome, in a specific region of the
chromosome, or at its precise location in
the chromosome’s DNA sequence.
 The
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2 main types of genome maps are
genetic maps and physical maps.
 Genetic maps are linkage maps. They
show the relative location of genes on a
chromosome as determined by
b
recombination frequencies.
 Distances on genetic maps are measured
in centimorgans (cM). One cM equals
0.01% recombination frequency.
Objective 16
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Objective 16
 Physical
maps show distances between
DNA landmarks. The resolution of
landmarks range from recognition sites
for restriction enzymes to the ultimate
level of detail: the actual DNA sequence.
 Distances between landmarks on a
physical map are measured in basebase-pairs
(1000 basebase-pairs equals 1 kilobase kb).
 The
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first physical maps were created by
cutting genomic DNA with different
restriction enzymes. The fragments were
then analyzed to determine their size and
how they fit together into a continuous
segment of the genome called a contig.
contig.
 Such a map shows the physical distance
between the different recognition sites of
the restriction enzymes:
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1
2. The fragments produced by
enzyme A only, by enzyme B only,
and by enzymes A and B
simultaneously are run out sideby-side on a gel, which separates
them according to size, smaller
fragments running faster
faster.
Objective 16
DNA
Molecular
weight
marker
14kb
10kb
6kb
2kb
3. The fragments are arranged so
that the smaller ones produced by
the simultaneous cut can be
grouped to generate the larger
ones produced by the individual
enzymes
4. A physical map is constructed.
 The
ultimate physical map of an
organism’s DNA is the actual basebase-pair
sequence of the entire genome.
 Although
g automated sequencers
q
have
been developed to determine the basebasepair sequence of DNA, they are only
accurate on fragments of DNA up to
about 500 basebase-pairs in length.
enzyme B
1. Multiple copies of a segment of
DNA are cut with restriction
enzymes.
14kb
9kb
8kb
9kb
5kb 5kb
3kb
2kb
2kb
2kb 8kb
9kb
A
A
5kb
14kb
B
2kb 3kb 5kb
9kb
A B
A
A B
A
2kb 5kb 10kb
19kb
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Objective 16
Clone-by-clone method
 In
order to sequence an entire
genome, which may contain billions of
base pairs, the DNA must be cut into
small fragments that can be sequenced
with automatic sequencers. There are
2 different ways to do this:
clone
clone--byby-clone sequencing
shotgun sequencing
1. Cut DNA segment into large fragments, then
determine the order of the large fragments by
identifying regions that overlap.
2. Cut each large
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fragment into smaller
fragments, then
sequence the small
fragments with an
automatic sequencer.
3. Determine the order of the small fragments
by identifying sequences that overlap.
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Objective # 17
Shotgun method
1. Cut DNA of entire
chromosome into small
fragments.
Discuss some of the main findings
of the Human Genome Project.
j
2. Sequence each small
fragment with an
automatic sequencer,
then order the fragments
based on overlapping
nucleotide sequences.
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Objective 17
Objective 17
The project to sequence the entire human
genome is called the human genome
project. This project has already led to
some important findings about genomes:
 The
Th h
human
m genome
m iis surprisingly
rpri i l
similar to other genomes. Many of the
genes in humans are identical or similar
to genes found in a wide variety of other
organisms from bacteria to chimps.
 Scientists
use computer analysis to
help locate genes within the DNA
sequence of the entire human genome.
The branch of biotechnology
gy that uses
computer analysis to search for genes,
to compare genomes, and to assemble
entire genomes from smaller
fragments is called bioinformatics.
bioinformatics.
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Objective 17
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 Although
eukaryotic genomes are much
larger and have many more genes than
prokaryotes, the size and complexity of
an organism is not directly related to the
number
b r off genes it has.
h F
Forr example,
pl
the human genome has around 25,000
genes, about the same number as mice
and far fewer than rice.
 Based
on current analysis, the human
genome seems to have far fewer genes
than expected. For many years
geneticists had estimated the number
of human genes to be around 100,000.
However, current research indicates
that the number is only around 25,000.
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Objective 17
Estimated Number o
of Genes
The size and complexity of an organism
is not directly related to the number of
genes it has:
prokaryotes
eukaryotes
50,000
 Genomes
Rice (Oryza sativa)
40,000
Puffer fish (Fugu rubripes)
Thale cress (Arabidopsis thaliana)
30,000
Fission yeast (Schizosaccharomyces pombe)
20,000
Bakers yeast (S. cerevisiae)
Protozoan
(Encephalitozoon
cuniculi)
10,000
Human (Homo sapiens)
Mouse (Mus musculus)
Nematode (Caenorhabditis elegans)
Mosquito (Anopheles sp.)
Fruit fly (Drosophila melanogaster)
Malaria microbe (Plasmodium falciparum)
Slime mold (Dictyostelium discoideum)
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0
1
10
100
1000
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10,000
contain both coding and
non-coding DNA. Surprisingly, only
nonabout 1.5% of the human genome
actually codes for proteins. Types of
coding
di DNA include:
i l d
 Single copy genes – many genes exist
as single copies on a particular
chromosome
Size of Genome (million base-pairs) Log Scale
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Objective 17
 Segmental
duplications – whole blocks
of genes that were copied from one
chromosome to another
 Multigene
g
families – ggroups
p of related
but distinctly different genes that often
occur close together. These related
genes seem to have arisen by the
duplication of a single ancestral gene:
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Objective 17
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 Tandem
clusters – these are identical
copies of the same gene that occur
near each other. They are transcribed
simultaneously , increasing the amount
of mRNA available for protein
synthesis. Tandem clusters also
include genes that do not encode
proteins, such as clusters of rRNA
genes.
 Most
DNA does not code for
proteins. Although its exact function
is not entirely clear, scientists have
recognized several types of nonnon-coding
DNA in humans:
 Introns (24% of genome) are non
non-coding regions that make up most of
each human gene.
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 Segmental
duplications (5% of genome)
are long nucleotide sequences that have
been duplicated and moved either
within a chromosome, or to a
nonhomologous chromosome
chromosome.
 Pseudogenes (2% of genome) seem like
normal protein
protein--coding genes that may
have lost their function due to
mutations.
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 Structural
DNA (20% of genome)
remains tightly coiled throughout the
cell cycle (constitutive heterochromatin)
and tends to be localized near the
centromeres and telomeres
telomeres.
 Simple sequence repeats (3% of
genome) are composed of a short
sequence of nucleotides that is repeated
thousands of times.
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Objective 17
 Transposable
elements or transposons
(45% of genome) are segments of
DNA that move around from one
location to another within the genome.
In some cases
cases, the transposon is
duplicated and the copy moves to a
new location. In other cases, the
transposon is removed from its
original location and is then inserted in
a new location.
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Objective 17
 Although
humans have only about
25,000 protein
protein--encoding genes, these
genes can code for at least 87,000
different proteins. How is this
possible?
 Alternative splicing of exons can
produce several different mature
mRNAs from a single gene:
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Alternative splicing of exons from the
same gene produces different mature
mRNAs and therefore different proteins
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Primary
y RNA transcript
p
5´ cap
mRNA splicing
exons
introns Processed RNA in brain
3 4 5 6 8 9 10 12
1 2 4 5 6 8 9 10 13
Mature mRNA in brain
5´ cap
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3´ poly-A tail
3´ poly-A tail
Processed RNA in muscle
Mature mRNA in muscle
5´ cap
3´poly-A tail
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Objective 17
the human genome is a
major step towards understanding the
genetic control of human traits.
 Among
g other benefits, it has the
potential to vastly improve the
prediction, diagnosis, prevention, and
treatment of disease in humans. The
practical applications of this
information will be enormous.
Objective # 18
 Sequencing
 Explain
what DNA microarrays
(biochips) are, and discuss their
usefulness to scientists.
scientists
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Objective 18
Objective 18
 Such
a chip can be used to screen a
genome for the presence of thousands
of specific alleles at once.
 To screen a person
person’ss genome,
genome a cDNA
sample is prepared, cut into fragments,
tagged with a fluorescent dye, and then
flooded over the chip.
A
DNA microarray,
microarray, is a small square
of glass that is covered with thousands
of short pieces of singlesingle-stranded
DNA arranged
rr
d iin a grid.
rid
 The short chains of DNA nucleotides,
which are attached to the glass surface,
are called oligonucleotides.
oligonucleotides.
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Objective 18
 By
determining which oligonucleotides
on the chip the cDNA binds to,
scientists can determine which specific
p
alleles are being expressed in the cells
that were used to prepare the cDNA:
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