Download Changes in chromosome structure (continued):

Chromosomes and chromosome rearrangements
Cytogenetics is the study of chromosomes and chromosome
rearrangements. This area of research is germane to several
areas of biological research.
Cytogenetics has been fundamental to understanding the
evolutionary history of a species (for example, although the
Chimp and the human are morphologically very different, at the
level of the chromosome (and DNA sequence) they are
extremely similar.
H = human
C= chimp
G = Gorilla
O = Orang utang
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Karyotype
Chromosomes are classified by size, centromere position and
banding pattern:
Shown below is the human karyotype (description of the
chromosome content of a given species)
Karyotype is the chromosome description of length, number,
morphology.
Karyotype analysis is extremely important in medicine.
Alternations in karyotypes are linked to birth defects and many
human cancers.
Metacentric- centromere in the middle
Acrocentric- centromere off center
telocentric centromere at one end
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Banding patterns
Specialized stains produce unique banding patterns along each
chromosome. Banding patterns are extremely useful for
detecting abnormalities in chromosome structure.
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Gross chromosomal changes
The Cri du chat syndrome in humans is a result of a deletion in
the short arm of chromosome 5. This was determined by
comparing banding patterns with normal and Cri du Chat
individuals
For many of the chromosome stains the molecular basis of the
banding patterns is unclear. Nonetheless these techniques
remain fundamental in many areas of genetic research
Types of chromosome rearrangements that can be studied by
karyotype analysis:
GROSS CHROMOSOMAL CHANGES
Deletions, Duplications, Inversions, Translocations
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DDIT
Normal Chromosome
A____B____C________D____E____F
Deletions (deficiency)
Duplications
Inversions
Translocation
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Deletions
Deletions are often detected cytologically by comparing
banding patterns between the normal and the partially
deleted chromosomes
Deleted
chromosome
Chromosome no
female
deletion
chromosome1
Band
46,XX, del(1)(q24q31)
Female with a deletion of chromosome 1 on the long arm (q)
between bands q24 to q31.
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In many instances deletions are too small to be detected
cytologically. In these instances genetic criteria are used.
Since deletions remove a contiguous set of genes, there is a
high probability that an essential gene will be deleted.
Therefore deletions will survive as heterozygotes and not
homozygotes.
Normal
Homologous deletion
(Lethal?)
Heterologous deletion
(NOT Lethal)
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A+_____B+_____C+___________D+
Normal
A+_____B+_____C+___________D+
In individuals heterozygous
for the deletion, pairing is
disrupted in the regions
surrounding the deletion.
Therefore recombination is
also significantly reduced in
these regions.
Normal
A deletion on one
homologue unmasks
recessive alleles on the
other homologue. The
effect is called pseudodominance.
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Deletions in X
Females in Drosophila
XX
Males in Drosophila
XY or XO
Deletion series
phenotype
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Changes in chromosome structure
Deletions:
1.
Homozygosity for large deletions results in lethalityeven the smallest cytologically defined deletions take out
tens of 1,000's of bps and are likely to remove essential
genes.
2. Organisms can tolerate heterozygosity for small but not
large deletions. The reason for this is not entirely clear
and is placed under the rubric of disrupting the overall
ratio of gene products produced by the organism
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Deletion mapping
Deficiency mapping or deletion mapping:
This provides a means of rapidly mapping a new mutation
A deficiency or deletion is the loss of a contiguous series
of nucleotides
ATGATCGGGCCCATCAAAAAAAAAAAATCATCCCCCGGGG
DELETION
ATGATCGGGCCCATC
CATCCCCCGGGG
ATGATCGGGCCCATC|CATCCCCCGGGG
Defined deficiencies are very useful for mapping genes
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Deficiency mapping
Say we have 6 sites defined by point mutations within
the rosy gene
---1-----2-----3-----4-----5-----6
------------------------------------------2--------------------------------------------4-------------------------DDDDDDDDDD---------Can we get intragenic recombinants that will restore
normal rosy gene?
ry2 and ry4?
Y
ry2 and the deletion?
Y
ry4 and the deletion
N
Say we isolate a new ry mutation you call it ry(zany)
You cross it to the deletion and do not find any
Recombinants
Where does ry(z) map
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Deficiency mapping
Generate a heterozygote
Gene point mutant/deletion mutant
Ask if you get intragenic recombinants
Heterozygote will be pseudodominant
The single point mutation will be observed over the deletion
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Multiple deficiencies
Specific deletions can define a series of regions within
a gene
Gene
---1-----2-----3-----4-----5-----6----7----8--
---------------------------------------------DDDDDDDDDDDDDDDDDDDDDDDDDDDDD----------------------------------DDDDDDDDDDDDDDDDDDDDDD------
These two deletions define 4 regions within the gene
I
II
III
IV
Now say a newly isolated mutation does not produce
normal recombinants with both deletions
To which region does it map?
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Duplications
A____B____C________D____E____F
A____B____C________D____E____E____F
normal
Duplication
Individuals bearing a duplication possess three copies of the genes
included in that duplication.
In general, for a given chromosomal region, organisms tolerate
duplications much better than deletions.
46,XY, dup(7)(q11.2q22)
Male with a duplication of chromosome 7 on the long arm (q)
between bands 11.2 to 22.
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Tandem duplications
This is a case in which the duplicated segment lies adjacent to
the original chromosomal segment
A B C D ------ A B C B C B C D
Once a tandem duplication arises in a population, even more
copies may arise because of asymmetrical pairing at meiosis.
Remember when the homologs pair during prophase of meiosis
I, they line up base-pair for base pair. Duplications lead to
mistakes in this pairing mechanism:
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Proper pairing:
A____B____C____B____C____D____E
A____B____C____B____C____D____E
A____B____C____B____C____D____E
A____B____C____B____C____D____E
Inappropriate pairing:
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Tandem duplications expand by mistakes in meiosis during
pairing
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19
The four meiotic products of a crossover between regions B
and C:
This process may repeat itself many times, such that a small
fragment of the genome is repeated 10,000 times.
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An example of this is near the centromeres of the Drosophila
genome:
If you look at the DNA sequence in this region it consists of
small 5-10 bp sequences (AATAC)n repeated 1,000s of times.
It is believed to have arisen from unequal crossing over.
Junk DNA
Selfish DNA
Conserved. Important?!
Heterochromatin
Genome sequence- Heterochromatin is usually not sequenced
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Duplications provide additional genetic material capable of
evolving new function. For example in the above situation if
the duplication for the B and C genes becomes fixed in the
population- the additional copies of B and C are free to evolve
new or modified functions.
This is one explanation for the origin of the tandemly
repeated hemoglobin genes in humans. Each of these has a
unique developmental expression pattern and provides a
specialized function.
The hemoglobin in fetus has a higher affinity for oxygen since
it acquires its oxygen from maternal hemoglobin via
competition
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Two distinct globin chains (each with its individual heme
molecule) combine to form hemoglobin.
One of the chains is designated alpha. The second chain is
called "non-alpha".
The fetus has a distinct non-alpha chain called gamma. After
birth, a different non-alpha globin chain, called beta, pairs
with the alpha chain. The combination of two alpha chains and
two non-alpha chains produces a complete hemoglobin molecule.
The genes that encode the alpha globin chains are on
chromosome 16. Those that encode the non-alpha globin
chains are on chromosome 11.
The alpha gene complex is called the "alpha globin locus",
The non-alpha complex is called the "beta globin locus".
The expression of the alpha and non-alpha genes is closely
balanced by an unknown mechanism. Balanced gene expression
is required for normal red cell function. Disruption of the
balance produces a disorder called thalassemia.
The closely linked
globin genes may have
originally arisen from
tandem duplication.
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Alternatively some duplicated genes accumulate mutations and
are no longer expressed (these are akin to junked cars along the
highway).
These are known as pseudogenes. One of the genes in the
hemoglobin cluster is a pseudogene.
-G-A-*--
pseudogene
Unequal crossing over among the tandemly repeated hemoglobin
gene cluster is the explanation for some inherited blood diseases.
Hemoglobin lepore
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***
•If mispairing in meiosis occurs, followed by a crossover between
delta and beta, the hemoglobin variant Hb-Lepore is formed.
• This is a gene that starts out delta and ends as beta. Since
the gene is controlled by DNA sequences upstream from the
gene, Hb-Lepore is expressed as if it were a delta. That is, it
is expressed at about 1% of the level that beta is expressed.
• Since normal beta globin is absent in Hb-Lepore, the person
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has severe anemia.
Inversion
Chromosomes in which two breaks occur and the resulting
fragment is rotated 180 degrees and reinserted into the
chromosome.
Inversions involve no change in the amount of genetic material
and therefore they are often genetically viable and show no
abnormalities at the phenotypic level.
Gene fusions may occur
Inversions are defined as to whether they span the centromere
Paracentric inversions do not span the centromere:
Pericentric inversions span the centromere:
In a pericentric inversion one break is in the short arm and one in
the long arm. Therefore an example might read
46,XY,inv(3)(p23q27).
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A paracenteric inversion does not include the centromere and an
example might be 46,XY,inv(1)(p12p31).
Homologs which are heterozygous for an inversion have
difficulties pairing in meiosis.
During pairing homologous regions associate with one another.
Consequently individuals heterozygous for an inversion will form
a structure known as an inversion loop.
Crossover within inverted region?
A---B---C---D---E---F---G
A’--B’---C’---D’--E’---F’--G’
A---B---C---D---E---F---G
A’--B’---C’--E’---D’---F’---G
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The consequence of crossover within a paricentric inversion
During meiosis, pairing leads to formation of an inversion loop
This is a problem if crossing over occurs within the inversion
As an exercise describe the consequence of crossover within a
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pericentric inversion (one that spans the centromere).
The consequence of crossover within a pericentric inversion
(one that spans the centromere).
During meiosis, pairing leads to formation of an inversion loop
This is a problem if crossing over occurs within the inversion
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•Paracentric inversion crosses over
with a normal chromosome, the
resulting chromosomes are an
acentric, with no centromeres, and
a dicentric, with 2 centromeres.
•The acentric chromosome isn't
attached to the spindle, so it gets
lost during cell division, and the
dicentric is usually pulled apart
(broken) by the spindle pulling the
two centromeres in opposite
directions. These conditions are
lethal.
•Pericentric inversion crosses over
with a normal chromosome, the
resulting chromosomes are
duplicated for some genes and
deleted for other genes. (They do
have 1 centromere apiece though).
•The gametes resulting from these
are aneuploid and do not survive.
•Thus, either kind of inversion has
lethal results when it crosses over
with a normal chromosome. The
only offspring that survive are
those that didn't have a
crossover. Thus when you count
the offspring you only see the
non-crossovers, so it appears that
crossing over has been suppressed.
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What are the consequences of crossing-over in an individual
homozygous for an inversion?
Genotype of an individual heterozygous for an inversion:
Genotype of an individual homozygous for an inversion:
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Translocations
A segment from one chromosome is exchanged with a segment
from another chromosome.
Chromosome 1
A
B
C
D
E
F
----------------------0-----------------------
Chromosome 2
O
P
Q
R
S
T
----------------------0-----------------------
Reciprocal translocation
A
B
C
D
S
T
----------------------0----------------------O
P
Q
R
E
F
----------------------0----------------------This is more specifically called a reciprocal translocation and
like inversions (and unlike duplications and deficiencies) no
genetic material is gained or lost in a reciprocal translocation.
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long arms of chromosome 7 and
21 have broken off and
switched places. So you can
see a normal 7 and 21, and a
translocated 7 and 21.
This individual has all the
material needed, just switched
around (translocated), so they
should have no health
problems. However there can
be a problem when this person
has children.
Remember that when the
gametes are made, each parent
gives one of each chromosome
pair. What would happen if this
person gave the normal seven
and the 21p with 7q attached?
t(11;18)(q21;q21) translocation between chromosomes 11 and 18
at bands q21 and q21
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Philadelphia chromosome: t(9;22)(q34;q11).
As with inversions, individuals heterozygous for a reciprocal
translocation will exhibit abnormalities in chromosome pairing
Notice this individual has the normal amount of genetic material
(two copies of each gene). However it is rearranged.
If the translocated fragment contains a centromere, you could get
dicentri and acentric chromosomes
How will translocated chromosomes pair in meiosis?
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Homologous regions associate with one another.
These chromosomes will follow Mendel's rule of independent of
assortment. In this instance one must focus on the centromere
There are two possible patterns of segregation.
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Alternate segregation:
ｷ
N1 and N2 segregate to one pole
ｷ
T1 and T2 segregate the other pole
These gametes have the normal haploid gene content: one copy
of each gene and are normal
Adjacent segregation:
ｷ
N1 and T1 segregate to one pole
ｷ
T2 and N2 segregate to the other pole
These gametes are anueploid: they are missing some genes and
duplicated for other genes.
Adjacent segregation
ｷ
N1 and T2 segregate to one pole
ｷ
N2 and T1 segregate to one pole
These forms of segregation are not equally frequent.
In a translocation heterozygote, some of the gametes are
viable and some are inviable.
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Reciprocal translocations result in genes that are known to map
to different chromosomes but behave as linked genes.
Under normal circumstances genes E and R assort independently
because they are on different chromosomes. However in a
translocation they will behave as closely linked genes and
segregate together.
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Translocations (and inversion) breakpoints sometimes disrupt an
essential gene. That is the break occurs in the middle of a
gene.
In fact because of this, a number of specific translocations are
causally associated with specific human cancers.
The inherited disease Duchenne muscular dystrophy was mapped
through a translocation that specifically disrupted this gene.
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Karyotypes and chromosome rearrangements
The Philadelphia chromosome:
This is a translocation involving chromosome 9 and 22
Individuals bearing this chromosome develop chronic
myelogenous leukemia.
First example of a chromosome translocation associated with
a human disease.
1
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