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Eukaryotic Chromosome
Organization — Lecture II
Dr. Steven J. Pittler
VH 375B
Office 4-6744
Cell 612-9720
13-1
Suggested Reading: Lewis 2nd
Edition
Chapter on Chromosomes
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Chromosomes
Structures that consists primarily of
DNA and proteins that are duplicated
and transmitted during mitosis or
meiosis
Heterochromatin stains dark and is
mostly repetitive DNA sequences
Euchromatin stains lighter and
contains protein encoding genes
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13-3
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Multiple Levels
of packing are
required to fit the
DNA into the cell
nucleus
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The basic unit
of chromatin
is the nucleosome
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The nucleosome consists of 146bp of DNA
wrapped around a protein core of 8 histones
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Histone H1 helps compact the
nucleosomes into a 30nm fiber
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The Histone
tails are a
critical
determinant of
chromatin
structure
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Specific modifications are associated with specific functions
13-9
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The normal karyotype:
23 diploid chromosomes
Human somatic cells contain 46 chromosomes:
paired homologs of chromosomes 1 to 22 and
sex chromosomes (XX or XY)
• Diploid refers to the presence of two copies of
each different chromosome.
• Gametes have one set of each chromosome
and are called haploid.
• Cells missing a single chromosome or having
an extra one are aneuploid
• Cells which contain a normal chromosome
constitution are called euploid.
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Karyotype analysis
Metaphase chromosomes are squashed on a slide and
stained with DNA binding dyes.
Banding patterns help define different chromosomes.
Chromosomes
were named in
order of their size
and centromere
position that
appear during
mitotic
metaphase.
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“Histone Code” hypothesis
Modifications of the Histone tails act as marks that
can be read by other proteins to control the expression or
replication of chromosomal regions. The coding in the
histones may be heritable.
E.g. Generally, histone acetylation is associated with
transcriptionally active genes
Deactylation is associated with inactive genes
(= gene silencing)
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Epigenetics
Heritable changes not caused by mutation
in the DNA
Can be due to stable changes in gene expression
caused by changes in chromatin structure
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Epigenetics and Disease:
Genomic imprinting
Parent specific expression or repression of genes
or chromosomes in offspring.
So… even though two copies of a given gene are inherited,
one from each parent, only the maternal or paternal allele
is expressed.
The non-expressed allele is said to be “imprinted.”
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Wilms Tumor
-Childhood Tumor of the kidney (nephroblastoma)
Accounts for 7% of all childhood cancers
-Caused by a defect in imprinting of the Insulin-like
Growth Factor 2 (IGF2) gene
-IGF2 is usually only expressed from the paternal locus, i.e.
maternally imprinted
-Defects in imprinting that cause expression of the maternal
locus lead to cancer
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DNA methylation
Covalent modification of the DNA is also
important for gene
silencing human cells
Most genes have GC rich areas of DNA in their
promoter
regions. These are referred to as CpG islands.
Methylation of the C residues within the CpG
islands leads
to gene silencing
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Epigenetics and Disease:
DNA methylation
Rett Syndrome: X-linked,
neurodegenerative disorder
affects 1:10,000-15,000 (females only)
Caused by a mutation in the gene
encoding
Methyl-CpG-binding protein 2
(MeCP2),
which in turn leads to loss of gene
silencing at many loci.
13-17
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The karyotype shows the chromosome
complement of a normal ________?
1. Male
2. Female
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Largest,
Metacentric
Smallest
acrocentric
Sex chromosomes
XX (shown)
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Anatomy of a chromosome
Chromosomes are
categorized by the
relative location of their
centromere.
•At tip - telocentric (not
found in humans)
•Close to tip - acrocentric
•At midpoint - metacentric
•Displaced from center submetacentric
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Anatomy of a chromosome
The portion of the
chromosome to each
side of a centromere is
called a chromosome
arm.
shorter arm = p arm
longer arm = q arm
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Anatomy of a chromosome
Telomeres are:
•At the tips of chromosomes
•Many repeats of the sequence TTAGGG
•Subtelomeres have more varied short
repeats
•These are the chromosomal parts between
protein-rich areas and the telomeres
•These areas extend from 8,000 to 30,000
bases inward toward the centromere from
the telomeres
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Subtelomeres
Include some protein-encoding genes and
bridge the gene-rich regions and the telomere
repeats
When researchers compared subtelomeres
to known gene sequences they found about
500 matches
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Anatomy of a chromosome
Centromeres are the largest constriction of the
chromosome
•Site of attachment of spindle fibers
•171 base pair segment repeated 100,000
times, called alpha satellite sequences
•Also include centromere-associated proteins
•Some are synthesized only when mitosis
is imminent forming the kinetochore that
emmanates from the centromere and
connects the spindle fibers
•Appears during prophase and vanishes
during telophase
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13-25
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Chromosomal shorthand
An ideogram represents a
chromosome schematically.
The major banding regions
are indicated with numbers.
Sucrose intolerance is
located at 3q.26
(chromosome 3, long arm,
major band 26)
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Chromosomes carry different genes
ideograms
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Visualizing chromosomes
• Obtain tissue from person
Fetal tissue: amniocentesis
chorionic villi sampling
fetal cell sorting
Adult tissue: blood (white blood cells)
cheek swab (buccal cells)
skin cells
tissue biopsy
• Prepare cells on slide to remove rest of cell matter
• Stain DNA with dyes or DNA probes (is a labeled piece
of DNA that binds to its complimentary sequence on a
particular chromosome) to visualize DNA
• Evaluate chromosomes in comparison to known
information
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FISHing
• Conventional chromosome stains have one
drawback- they are not specific to a particular
chromosome
• FISH uses DNA probes that are complimentary
to specific base sequences, and if those
sequences are unique to a particular
chromosome the technique can identify it
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FISH: fluorescence in situ hybridization
DNA probes labelled with fluorescing dye bind
complementary DNA
13-30
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Cytogenetics
the subdiscipline within genetics
that focuses on chromosome variations.
Abnormal number of copies of genes or
chromosomes can lead to genetic
abnormalities.
13-31
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Mutation at the Chromosome Level
 Abnormal numbers of genes or chromosomes
 Range from the single-base changes to missing or extra pieces
of chromosomes
 A mutation is a chromosomal aberration if it is large enough to
see with a light microscope using stains and/or fluorescent tags
 Generally, excess genetic material has a milder effect on human
health when compared to a deficit of genetic material
 Most chromosomal abnormalities are so severe that prenatal
development ceases in the embryo
 0.65 percent of all newborns have chromosomal aberrations
 An additional 0.20 percent have chromosomal rearrangements
that do not produce symptoms
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Chromosomal Abnormalities
• Down syndrome-extra chromosome 21
• Turner syndrome- XO- a female with only one
X chromosome
• Klinefelter syndrome- XXY, a male with an
extra X chromosome
– Before this women who were XO were thought to
be genetic males because they lack Barr bodies
and XXY were thought to be genetic females
because their cells have Barr bodies
13-33
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Chromosome anomalies
may cause phenotype abnormalities.
This young girl has Down syndrome.
A chromosome karyotype revealed she carries three
copies of chromosome 21, a condition called trisomy 21.
13-34
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Extra Autosomes
 Chromosomes 13, 18, and 21 are the most
frequently seen extra autosomes and they have
the lowest gene densities- they carry
considerably fewer protein-encoding genes
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Chromosomal shorthand
Abbreviation
What it means
46, XY
Normal male
46, XX
Normal female
45, X
Turner syndrome female
47, XXY
Klinefelter syndrome male
47, XYY
Jacobs syndrome male
46, XY del (7q)
Male missing part of long arm of
chromosome 7
47, XX+21
Female with trisomy 21
46, XY t (7;9)
(p21.1;q34.1)
Male with translocation between short
arm of chromosome 7 at band 21.1 and
long arm of chromosome 9 at band 34.1
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Chromosome Abnormalities
Polyploidy
Aneuploidy
monosomy
trisomy
Deletion
Duplication
Inversion
Translocation
Iso chromosome
Ring chromosome
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Extra chromosome set
Extra or missing chromosome
one chromosome absent
one chromosome extra
Part of a chromosome missing
Part of a chromosome present twice
Segment of chromosome reversed
Two chromosome arms exchanged
in part or entirely
A chromosome with identical arms
A chromosome that forms a ring
due to deletions in telomeres,
which cause ends to adhere
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Polyploidy
Individuals with three copies
of each chromosome are
triploid, or an extra set
•Polyploidy accounts for 17%
of all spontaneous abortions
and 3% of stillbirths/newborn
deaths.
Result of:
•Two sperm fertilize one egg.
•Haploid sperm fertilizes
diploid egg.
13-38
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Aneuploidy
• Most autosomal aneuploids are spontaneously aborted
•Mental retardation is common in an individual who
survives aneuploidy
•Sex chromosome aneuploidy have milder symptoms
•Children born with the wrong number of chromosomes
have an extra chromosome- trisomy
•Rather than missing a chromosome- monosomy
•Down syndrome can result from trisomy 21 or from
translocation
•Translocation Down syndrome accounts for 4% of
cases, has a much higher risk of recurrence than
trisomy 21
13-39
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Aneuploidy
•Nondisjunction is a common cause of aneuploidy
resulting in a gamete with one extra chromosome and
another gamete with one missing chromosome.
•Nondisjunction during the first meiotic anaphase
division results in a copy of each homolog in the
gamete and two cells do not have any copies.
•Nondisjunction during the second meiotic anaphase
division results in both sister chromatids in one gamete,
one with no copy, and two normal cells.
13-40
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Nondisjunction causes aneuploidy
Nondisjunction
in meiosis I
Anaphase I
Anaphase II
Nondisjunction
in meiosis II
Gametes
13-41
Abnormal gametes
Abnormal gametes Normal gametes
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Trisomies and Monosomies
One extra or one missing chromosome results in extra or
missing copies of all of the genes on that chromosome.
Most trisomies and monosomies produce inviable embryos.
Some fetuses with trisomy of smaller autosomes survive to
birth with syndromic conditions:
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trisomy
(syndrome)
% conceptions that
survive >1 year
Incidence at birth
13 (Patau)
1/12,500 to 1/21,700
<5%
18 (Edward)
1/6,000 to 1/10,000
< 5%
21 (Down)
1/800 to 1/826
85%
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Autosomal Aneuploids
• Most autosomal aneuploids are lethal
• Trisomy 21 Down syndrome
– Most common
– Extra folds in the eyelids called epicanthal folds
and a flat face
– Termed mongoloid by Sir John Langdon Haydon in
1866
– In 1961, researchers identified a mosaic Down
syndrome
• Affected girl with all the physical signs but normal
intelligence
13-43
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Autosomal Aneuploids
• Trisomy 21 cont’d
• Usually short and has straight, sparse hair, and a
thick tongue protruding through the lips
• Hands have abnormal pattern of creases, loose joints,
and poor reflexes and muscle tone give a floppy
appearance
• Intelligence varies
• Physical problems are common
–
–
–
–
13-44
Heart and kidney defects, and hearing and vision loss
Suppressed immune system
Digestive system problems
Down syndrome 15 is more likely to develop leukemia
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Autosomal Aneuploids
•
•
•
•
Trisomy 18- Edward Syndrome
Only 1 in 6,000 -10,000 newborns have trisomy 18
Most do not survive birth
Great physical and mental disabilities, with
developmental skills stalled at the six-month level
• Major abnormalities
– Heart defects, displaced liver, growth retardation, and
oddly clenched fists
– Overlapping placement of fingers, narrow and flat skull,
abnormally shaped and low-set ears, small mouth and
face, unusual or absent fingerprints, short large toes
with fused second or third toes, and “rocker-bottom”
feet
– Most cases are attributed to non-disjunction in meiosis
II of the oocyte
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Oddly
clenched
fist
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Autosomal Aneuploids
• Trisomy 13- Patau Syndrome
• Most do not survive birth
• Most striking but quite rare is fusion of the developing
eyes, so that the fetus has one large eyelike structure
in the center of the face
• More common is a small or absent eye
• Major abnormalities
– Heart defects, kidneys, brain, face, and limbs
– The nose is malformed, and cleft lip and/or present in a
small head
– Extra fingers and toes
– Extra spleen, abnormal liver, rotated intestines, and an
abnormal pancreas
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Sex Chromosome Aneuploidy
Situation
Normal
Female
Nondisjunction
Oocyte
Sperm
Consequence
X
Y
46, XY normal male
X
X
46, XX normal female
XX
Y
47, XXY Klinefelter syndrome
XX
X
47, XXX triplo-X
Y
45, Y nonviable
X
45, X Turner syndrome
Male
Nondisjunction
(meiosis I)
X
X
XX
47, XXX triplo-X
Male
nondisjunction
(meiosis II)
X
YY
47, XYY Jacobs syndrome
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X
45, X Turner syndrome
45, X Turner syndrome
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Turner syndrome
45, X
1 in 2,000 female births
99% of Turner die in utero
• Absence of Y leads to development as a
female.
• Absence of two copies of X-linked genes in a
female results in Turner syndrome.
Phenotypes include short stature, webbing at
back of neck, incomplete sexual development,
hearing impairment, malformed eyebrows.
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Turner syndrome
• A chromosomal imbalance causes the hormone
deficit
• 1954 P.E. Polani discovered cells from Turner
syndrome patients lack a Barr body (inactive X)
• 50% are XO, the rest have partial deletions or are
mosaics, with only some cells affected
• Like autosomal aneuploidy this syndrome is more
frequent among spontaneously aborted fetus than
newborns
• Two X chromosomes are necessary for normal
sexual development
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Triplo-X aneuploidy
47, XXX
1 in 1,000 female births
Extra copy of every X-linked gene
Few modest effects on phenotype include
tallness, menstrual irregularities and slight
impact on intelligence- less intelligent than
their siblings
X-inactivation of two X chromosomes occurs
while third remains active seems to
compensate for presence of extra X
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Klinefelter syndrome
47, XXY
1 in 1,000 male births
Extra copy of each X-linked gene
• Phenotypes include incomplete sexual
development (rudimentary testes and prostate),
long limbs, large hands and feet, some breast
tissue development, and they are infertile.
• Some cases are not diagnosed until fertility
problems arise or remain undiagnosed.
Look at reading
on page 256
13-52
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XYY syndrome
47, XYY (Jacobs Syndrome)
1 in 1,000 male births
Extra Y chromosome
96% phenotypically normal
• Modest phenotypes may include great
height, acne and minor speech and
reading problems.
• Studies suggesting some increase in
aggressive behaviors remain
controversial.
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Chromosome structural abnormalities
Chromosomal deletions or duplications result in
extra or missing copies of genes in the involved
segment.
13-54
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Chromosome Deletions
• Is missing genetic material
– Cri-du-chat syndrome
• Caused by deletion of part of the short arm of
chromosome 5 (5p- syndrome)
• High-pitch cry that resembles mewing of a cat
• Pinched facial features, developmentally delayed, and
mentally retarded
• Removes the gene for telomerase reverse transcriptase
• Shortened lifespan
• Low birth weight, poor muscle tone, small head, and
impaired language skills
• Reading page 258
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Duplication
• Is a region of a chromosome where genes are
repeated
• Causes symptoms if they are extensive
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Larger duplications lead to more severe phenotype
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Translocation
Different nonhomologous chromosome exchange
portions of chromosomes or combined parts
Two major types:
Robertsonian translocation
•Two nonhomologous acrocentric chromosomes
break at the centromere and long arms fuse. The
short arms are often lost.
•5% of Down syndrome results from a Robertsonian
translocation between chr 21 and chr 14 .
Reciprocal translocation
•Two nonhomologous chromosomes exchange a
portion of their chromosome arms.
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Reciprocal translocation
Exchange of material from one chromosome arm to
another is called a reciprocal translocation.
Rearrangement of the genetic material results in an
individual who carries a translocation but is not
missing any genetic material unless a translocation
breakpoint interrupts a gene.
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Reciprocal translocation
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Reciprocal Translocations
• Translocation between chromosome 2 and 20 causes
Alagile syndrome
– The exchange disrupts a gene on chr 20 that causes the
condition
– Produces a characteristic face, absence of bile ducts in
the liver, abnormalities of the eyes and ribs, heart
defects, and severe itching
• Translocation between chromosomes 12 and 22
– Language delay, mild mental retardation, loose joints,
minor facial anomalies, and a narrow, long head:
matched those of 22q13.3 deletion syndrome
– Caused by the absence of ProSAP2 because the
translocation cuts the gene
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Reciprocal Translocation 2:20
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Inversions
Inverted chromosomes have a region flipped in
orientation compared to wild type chromosomes.
• 5-10% cause health problems probably due to disruption
of genes at the breakpoints.
• Crossing over within the inverted segments leads to
genetically imbalanced gametes.
Two types of inversions occur:
Paracentric - inverted region does NOT include
centromere
Pericentric - inverted region includes centromere
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Segregation of a paracentric inversion
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Segregation of a pericentric inversion
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Isochromosomes
Chromosomes with
identical arms form
when centromeres
divide along the
incorrect plane during
meiosis.
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Ring chromosomes
• Chromosomes shaped like a ring occur in
1 of 25,000 conceptions.
• May arise when telomeres are lost and
sticky chromosome ends fuse.
• Ring chromosomes have phenotypes
associated with the loss or addition of
genetic material.
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Causes of chromosomal abnormalities
Polyploidy Error in cell division in which all chromatids fail
to separate at anaphase. Multiple fertilizations.
Aneuploidy Nondisjunction leading to extra or lost
chromosomes
Deletions and Translocations.
duplications Crossover between a pericentric inversion and
normal homologue
Translocation Recombination between nonhomologous
chromosomes
Inversion Breakage and reunion with wrong orientation
Dicentric or Crossover between paracentric inversion and
acentric fragments normal homologue.
Isochromosome Division of centromeres on wrong plane
Ring chromosome Loss of telomeres and fusion of ends
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