Chromosomes and chromosome rearrangements

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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 gorilla 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
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 pseudo-dominance. Hemizygous
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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
• Homozygosity for large deletions results in
  lethality- even 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
ATGATCGGGCCCATCCATCCCCCGGGG
Defined deficiencies are very useful for mapping
genes
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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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Duplications
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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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
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
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Tandem duplications expand by mistakes in meiosis
during pairing
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(No Transcript)
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A
B
C
B
C
D
A
B
C
B
C
D
C
B
B
C
B
A
C
B
D
A
C
D
A
B
C
B
C
D
A
B
C
B
C
B
C
D
A
B
C
D
A
B
C
B
C
D
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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. 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?! Heterochro
matin 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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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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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). A
paracenteric inversion does not include the
centromere and an example might be
46,XY,inv(1)(p12p31).
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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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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 pericentric inversion (one
that spans the centromere).
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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(1118)(q21q21) translocation between
chromosomes 11 and 18 at bands q21 and
q21 Philadelphia chromosome t(922)(q34q11).
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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?
There are three copies of 7q instead of two. And
there is only one copy of 21q
t(1118)(q21q21) translocation between
chromosomes 11 and 18 at bands q21 and
q21 Philadelphia chromosome t(922)(q34q11).
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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 ? N1 and N2 segregate to
one pole ? 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 ? N1 and T1
segregate to one pole ? T2 and N2 segregate to
the other pole These gametes are anueploid they
are missing some genes and duplicated for other
genes. These forms of segregation are equally
frequent. Therefore, in a translocation
heterozygote, about 50 of the gametes are viable
and 50 are unviable.
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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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abl/bcr Fusion protein Chronic myelogenous and
acute lymphotic leukemia ALK/NPM Fusion
Large cell lymphomas bcr/abl Fusion
Chronic myelogenous/acute lymphotic
leukemia HER2/neu Fusion Breast and cervical
carcinomas MYH11/CBFB Fusion Acute myeloid
leukemia ML/RAR Fusion Acute premyelocytic
leukemia ERG/TMPRSS2 Fusion prostate cancer
Gene fusion -prostate cancer -ERG merges with a
prostate-specific gene called TMPRSS2. ERG is a
transcription factors