Karyotype

From Wikipedia, the free encyclopedia

A karyotype is the number and appearance of chromosomes in the nucleus of a

eukaryotic cell.[1][2]p28[3] The term is also used for the complete set of chromosomes in
a species, or an individual organism.

Karyotypes describe the number of chromosomes, and what they look like under a light
microscope. Attention is paid to their length, the position of the centromeres, banding
pattern, any differences between the sex chromosomes, and any other physical
characteristics.[4] The preparation and study of karyotypes is part of cytogenetics.

Karyogram of human male using Giemsa staining.

The study of whole sets of chromosomes is sometimes known as karyology. The

chromosomes are depicted (by rearranging a microphotograph) in a standard format
known as a karyogram or idiogram: in pairs, ordered by size and position of centromere
for chromosomes of the same size.

The basic number of chromosomes in the somatic cells of an individual or a species is

called the somatic number and is designated 2n. Thus, in humans 2n = 46. In the germ-
line (the sex cells) the chromosome number is n (humans: n = 23).[2]p28

So, in normal diploid organisms, autosomal chromosomes are present in two copies.
There may, or may not, be sex chromosomes. Polyploid cells have multiple copies of
chromosomes and haploid cells have single copies.

Karyotypes can be used for many purposes; such as, to study chromosomal aberrations,
cellular function, taxonomic relationships, and to gather information about past
evolutionary events.Contents [hide]
1 History of karyotype studies
2 Observations on karyotypes
2.1 Staining
2.2 Observations
2.3 The human karyotype
3 Diversity and evolution of karyotypes
3.1 Changes during development
3.2 Number of chromosomes in a set
3.3 Fundamental number
3.4 Ploidy
3.5 Aneuploidy
3.6 Chromosomal polymorphism
3.7 Species trees
4 Depiction of karyotypes
4.1 Types of banding
4.2 Classic karyotype cytogenetics
4.3 Spectral karyotype (SKY technique)
4.4 Digital karyotyping
5 Chromosome abnormalities
6 See also
7 References
8 External links

[edit]
History of karyotype studies

Chromosomes were first observed in plant cells by Karl Wilhelm von Nägeli in 1842.
Their behavior in animal (salamander) cells was described by Walther Flemming, the
discoverer of mitosis, in 1882. The name was coined by another German anatomist, von
Waldeyer in 1888.

The next stage took place after the development of genetics in the early 20th century,
when it was appreciated that the set of chromosomes (the karyotype) was the carrier of
the genes. Levitsky seems to have been the first to define the karyotype as the phenotypic
appearance of the somatic chromosomes, in contrast to their genic contents.[5][6] The
subsequent history of the concept can be followed in the works of Darlington[7] and
White.[2][8]

Investigation into the human karyotype took many years to settle the most basic question:
how many chromosomes does a normal diploid human cell contain?[9] In 1912, Hans
von Winiwarter reported 47 chromosomes in spermatogonia and 48 in oogonia,
concluding an XX/XO sex determination mechanism.[10] Painter in 1922 was not certain
whether the diploid number of humans was 46 or 48, at first favouring 46.[11] He revised
his opinion later from 46 to 48, and he correctly insisted on humans having an XX/XY
system.[12] Considering their techniques, these results were quite remarkable.

New techniques were needed to definitively solve the problem:

Using cells in culture
Pretreating cells in a hypotonic solution, which swells them and spreads the
chromosomes
Arresting mitosis in metaphase by a solution of colchicine
Squashing the preparation on the slide forcing the chromosomes into a single plane
Cutting up a photomicrograph and arranging the result into an indisputable karyogram.

It took until the mid 1950s until it became generally accepted that the karyotype of
humans included only 46 chromosomes.[13][14] Rather interestingly, the great apes have
48 chromosomes. Human chromosome 2 was formed by a merger of ancestral
chromosomes, reducing the number.
[edit]
Observations on karyotypes
[edit]
Staining
The study of karyotypes is made possible by staining. Usually, a suitable dye, such as
Giemsa,[15] is applied after cells have been arrested during cell division by a solution of
colchicine. For humans, white blood cells are used most frequently because they are
easily induced to divide and grow in tissue culture.[16] Sometimes observations may be
made on non-dividing (interphase) cells. The sex of an unborn fetus can be determined by
observation of interphase cells (see amniotic centesis and Barr body).
[edit]
Observations

Six different characteristics of karyotypes are usually observed and compared:[17]

Differences in absolute sizes of chromosomes. Chromosomes can vary in absolute size by
as much as twenty-fold between genera of the same family: Lotus tenuis and Vicia faba
(legumes), both have six pairs of chromosomes (n=6) yet V. faba chromosomes are many
times larger. This feature probably reflects different amounts of DNA duplication.
Differences in the position of centromeres. This is brought about by translocations.
Differences in relative size of chromosomes can only be caused by segmental interchange
of unequal lengths.
Differences in basic number of chromosomes may occur due to successive unequal
translocations which finally remove all the essential genetic material from a chromosome,
permitting its loss without penalty to the organism (the dislocation hypothesis). Humans
have one pair fewer chromosomes than the great apes, but the genes have been mostly
translocated (added) to other chromosomes.
Differences in number and position of satellites, which (when they occur) are small
bodies attached to a chromosome by a thin thread.
Differences in degree and distribution of heterochromatic regions. Heterochromatin stains
darker than euchromatin, indicating tighter packing, and mainly consists of genetically
inactive repetitive DNA sequences.

A full account of a karyotype may therefore include the number, type, shape and banding
of the chromosomes, as well as other cytogenetic information.

Variation is often found:

Between the sexes
Between the germ-line and soma (between gametes and the rest of the body)
Between members of a population (chromosome polymorphism)
Geographical variation between races
Mosaics or otherwise abnormal individuals.[8]
[edit]
The human karyotype

Most (but not all) species have a standard karyotype. The normal human karyotypes
contain 22 pairs of autosomal chromosomes and one pair of sex chromosomes. Normal
karyotypes for females contain two X chromosomes and are denoted 46,XX; males have
both an X and a Y chromosome denoted 46,XY. Any variation from the standard
karyotype may lead to developmental abnormalities.
[edit]
Diversity and evolution of karyotypes

Although the replication and transcription of DNA is highly standardized in eukaryotes,

the same cannot be said for their karyotypes, which are highly variable. There is variation
between species in chromosome number, and in detailed organization, despite their
construction from the same macromolecules. This variation provides the basis for a range
of studies in evolutionary cytology.

In some cases there is even significant variation within species. In a review, Godfrey and
Masters conclude:
"In our view, it is unlikely that one process or the other can independently account for the
wide range of karyotype structures that are observed... But, used in conjunction with
other phylogenetic data, karyotypic fissioning may help to explain dramatic differences in
diploid numbers between closely related species, which were previously inexplicable.[18]

Although much is known about karyotypes at the descriptive level, and it is clear that
changes in karyotype organization has had effects on the evolutionary course of many
species, it is quite unclear what the general significance might be.
"We have a very poor understanding of the causes of karyotype evolution, despite many
careful investigations... the general significance of karyotype evolution is obscure."
Maynard Smith.[19]
[edit]
Changes during development

Instead of the usual gene repression, some organisms go in for large-scale elimination of
heterochromatin, or other kinds of visible adjustment to the karyotype.
Chromosome elimination. In some species, as in many sciarid flies, entire chromosomes
are eliminated during development.[20]
Chromatin diminution (founding father: Theodor Boveri). In this process, found in some
copepods and roundworms such as Ascaris suum, portions of the chromosomes are cast
away in particular cells. This process is a carefully organised genome rearrangement
where new telomeres are constructed and certain heterochromatin regions are lost.[21]
[22] In A. suum, all the somatic cell precursors undergo chromatin diminution.[23]
X-inactivation. The inactivation of one X chromosome takes place during the early
development of mammals (see Barr body and dosage compensation). In placental
mammals, the inactivation is random as between the two Xs; thus the mammalian female
is a mosaic in respect of her X chromosomes. In marsupials it is always the paternal X
which is inactivated. In human females some 15% of somatic cells escape inactivation.
[24]
[edit]
Number of chromosomes in a set

A spectacular example of variability between closely related species is the muntjac,

which was investigated by Kurt Benirschke and his colleague Doris Wurster. The diploid
number of the Chinese muntjac, Muntiacus reevesi, was found to be 46, all telocentric.
When they looked at the karyotype of the closely related Indian muntjac, Muntiacus
muntjak, they were astonished to find it had female = 6, male = 7 chromosomes.[25]
"They simply could not believe what they saw... They kept quiet for two or three years
because they thought something was wrong with their tissue culture... But when they
obtained a couple more specimens they confirmed [their findings]" Hsu p73-4[14]

The number of chromosomes in the karyotype between (relatively) unrelated species is

hugely variable. The low record is held by the nematode Parascaris univalens, where the
haploid n = 1; the high record would be somewhere amongst the ferns, with the Adder's
Tongue Fern Ophioglossum ahead with an average of 1262 chromosomes.[26] Top score
for animals might be the shortnose sturgeon Acipenser brevirostrum at a mere 372
chromosomes.[27] The existence of supernumerary or B chromosomes means that
chromosome number can vary even within one interbreeding population; and aneuploids
are another example, though in this case they would not be regarded as normal members
of the population.
[edit]
Fundamental number

The fundamental number, FN, of a karyotype is the number of visible major

chromosomal arms per set of chromosomes.[28][29] Thus, FN ≤ 2n, the difference
depending on the number of chromosomes considered single-armed (acrocentric or
telocentric) present. Humans have FN = 82,[30] due to the presence of five acrocentric
chromosome pairs (13, 14, 15, 21 and 22).
[edit]
Ploidy

Ploidy is the number of complete sets of chromosomes in a cell.

Polyploidy, where there are more than two sets of homologous chromosomes in the cells,
occurs mainly in plants. It has been of major significance in plant evolution according to
Stebbins.[31][32][33][34] The proportion of flowering plants which are polyploid was
estimated by Stebbins to be 30-35%, but in grasses the average is much higher, about
70%.[35] Polyploidy in lower plants (ferns, horsetails and psilotales) is also common,
and some species of ferns have reached levels of polyploidy far in excess of the highest
levels known in flowering plants.
Polyploidy in animals is much less common, but it has been significant in some groups.
[36]
Polyploid series in related species which consist entirely of multiples of a single basic
number are known as euploid.
Haplo-diploidy, where one sex is diploid, and the other haploid. It is a common
arrangement in the Hymenoptera, and in some other groups.
Endopolyploidy occurs when in adult differentiated tissues the cells have ceased to divide
by mitosis, but the nuclei contain more than the original somatic number of
chromosomes.[37] In the endocycle (endomitosis or endoreduplication) chromosomes in
a 'resting' nucleus undergo reduplication, the daughter chromosomes separating from
each other inside an intact nuclear membrane.[38]
In many instances, endopolyploid nuclei contain tens of thousands of chromosomes
(which cannot be exactly counted). The cells do not always contain exact multiples
(powers of two), which is why the simple definition 'an increase in the number of
chromosome sets caused by replication without cell division' is not quite accurate.
This process (especially studied in insects and some higher plants such as maize) may be
a developmental strategy for increasing the productivity of tissues which are highly active
in biosynthesis.[39]
The phenomenon occurs sporadically throughout the eukaryote kingdom from protozoa
to man; it is diverse and complex, and serves differentiation and morphogenesis in many
ways.[40]
See palaeopolyploidy for the investigation of ancient karyotype duplications.
[edit]
Aneuploidy

Aneuploidy is the condition in which the chromosome number in the cells is not the
typical number for the species. This would give rise to a chromosome abnormality such
as an extra chromosome or one or more chromosomes lost. Abnormalities in
chromosome number usually cause a defect in development. Down syndrome and Turner
syndrome are examples of this.

Aneuploidy may also occur within a group of closely related species. Classic examples in
plants are the genus Crepis, where the gametic (= haploid) numbers form the series x = 3,
4, 5, 6, and 7; and Crocus, where every number from x = 3 to x = 15 is represented by at
least one species. Evidence of various kinds shows that that trends of evolution have gone
in different directions in different groups.[41] Closer to home, the great apes have 24x2
chromosomes whereas humans have 23x2. Human chromosome 2 was formed by a
merger of ancestral chromosomes, reducing the number.[42]
[edit]
Chromosomal polymorphism

Some animal species are polymorphic for chromosome fusions or dissociations.[43]

When this happens, the chromosome number is variable from one individual to another.
Well-researched examples are the ladybird beetle Chilocorus stigma, some mantids of the
genus Ameles, the European shrew Sorex araneus. There is some evidence from the case
of the mollusc Thais lapillus (the dog whelk) on the Brittany coast, that the two
chromosome morphs are adapted to different habitats.[44]
[edit]
Species trees

The detailed study of chromosome banding in insects with polytene chromosomes can
reveal relationships between closely related species: the classic example is the study of
chromosome banding in Hawaiian drosophilids by Hampton Carson.

In about 6,500 sq mi (17,000 km2), the Hawaiian Islands have the most diverse collection
of drosophilid flies in the world, living from rainforests to subalpine meadows. These
roughly 800 Hawaiian drosophilid species are usually assigned to two genera, Drosophila
and Scaptomyza, in the family Drosophilidae.

The polytene banding of the 'picture wing' group, the best-studied group of Hawaiian
drosophilids, enabled Carson to work out the evolutionary tree long before genome
analysis was practicable. In a sense, gene arrangements are visible in the banding patterns
of each chromosome. Chromosome rearrangements, especially inversions, make it
possible to see which species are closely related.

The results are clear. The inversions, when plotted in tree form (and independent of all
other information), show a clear "flow" of species from older to newer islands. There are
also cases of colonization back to older islands, and skipping of islands, but these are
much less frequent. Using K-Ar dating, the present islands date from 0.4 million years
ago (mya) (Mauna Kea) to 10mya (Necker). The oldest member of the Hawaiian
archipelago still above the sea is Kure Atoll, which can be dated to 30 mya. The
archipelago itself (produced by the Pacific plate moving over a hot spot) has existed for
far longer, at least into the Cretaceous. Previous islands now beneath the sea (guyots)
form the Emperor Seamount Chain.[45]

All of the native Drosophila and Scaptomyza species in Hawaiʻi have apparently
descended from a single ancestral species that colonized the islands, probably 20 million
years ago. The subsequent adaptive radiation was spurred by a lack of competition and a
wide variety of niches. Although it would be possible for a single gravid female to
colonise an island, it is more likely to have been a group from the same species.[46][47]
[48][49]

There are other animals and plants on the Hawaiian archipelago which have undergone
similar, if less spectacular, adaptive radiations.[50][51]
[edit]
Depiction of karyotypes
[edit]
Types of banding

Cytogenetics employs several techniques to visualize different aspects of chromosomes:

[16]
G-banding is obtained with Giemsa stain following digestion of chromosomes with
trypsin. It yields a series of lightly and darkly stained bands - the dark regions tend to be
heterochromatic, late-replicating and AT rich. The light regions tend to be euchromatic,
early-replicating and GC rich. This method will normally produce 300-400 bands in a
normal, human genome.
R-banding is the reverse of G-banding (the R stands for "reverse"). The dark regions are
euchromatic (guanine-cytosine rich regions) and the bright regions are heterochromatic
(thymine-adenine rich regions).
C-banding: Giemsa binds to constitutive heterochromatin, so it stains centromeres.
Q-banding is a fluorescent pattern obtained using quinacrine for staining. The pattern of
bands is very similar to that seen in G-banding.
T-banding: visualize telomeres.
Silver staining: Silver nitrate stains the nucleolar organization region-associated protein.
This yields a dark region where the silver is deposited, denoting the activity of rRNA
genes within the NOR.
[edit]
Classic karyotype cytogenetics

Karyogram from a human female lymphocyte probed for the Alu sequence using FISH.

In the "classic" (depicted) karyotype, a dye, often Giemsa (G-banding), less frequently
Quinacrine, is used to stain bands on the chromosomes. Giemsa is specific for the
phosphate groups of DNA. Quinacrine binds to the adenine-thymine-rich regions. Each
chromosome has a characteristic banding pattern that helps to identify them; both
chromosomes in a pair will have the same banding pattern.

Karyotypes are arranged with the short arm of the chromosome on top, and the long arm
on the bottom. Some karyotypes call the short and long arms p and q, respectively. In
addition, the differently stained regions and sub-regions are given numerical designations
from proximal to distal on the chromosome arms. For example, Cri du chat syndrome
involves a deletion on the short arm of chromosome 5. It is written as 46,XX,5p-. The
critical region for this syndrome is deletion of 15.2, which is written as 46,XX,del(5)
(p15.2).[52]
[edit]
Spectral karyotype (SKY technique)

Spectral karyogram of a human female

Spectral karyotyping is a molecular cytogenetic technique used to simultaneously

visualize all the pairs of chromosomes in an organism in different colors. Fluorescently
labeled probes for each chromosome are made by labeling chromosome-specific DNA
with different fluorophores. Because there are a limited number of spectrally-distinct
fluorophores, a combinatorial labeling method is used to generate many different colors.
Spectral differences generated by combinatorial labeling are captured and analyzed by
using an interferometer attached to a fluorescence microscope. Image processing
software then assigns a pseudo color to each spectrally different combination, allowing
the visualization of the individually colored chromosomes.[53]

Spectral human karyotype

This technique is used to identify structural chromosome aberrations in cancer cells and
other disease conditions when Giemsa banding or other techniques are not accurate
enough.
[edit]
Digital karyotyping
Digital karyotyping is a technique used to quantify the DNA copy number on a genomic
scale. Short sequences of DNA from specific loci all over the genome are isolated and
enumerated.[54] This is method is also known as virtual karyotyping.
[edit]
Chromosome abnormalities
Main article: Chromosome abnormalities

Chromosome abnormalities can be numerical, as in the presence of extra or missing

chromosomes, or structural, as in derivative chromosome, translocations, inversions,
large-scale deletions or duplications. Numerical abnormalities, also known as aneuploidy,
often occur as a result of nondisjunction during meiosis in the formation of a gamete;
trisomies, in which three copies of a chromosome are present instead of the usual two, are
common numerical abnormalities. Structural abnormalities often arise from errors in
homologous recombination. Both types of abnormalities can occur in gametes and
therefore will be present in all cells of an affected person's body, or they can occur during
mitosis and give rise to a genetic mosaic individual who has some normal and some
abnormal cells.

Chromosomal abnormalities that lead to disease in humans include

Turner syndrome results from a single X chromosome (45, X or 45, X0).
Klinefelter syndrome, the most common male chromosomal disease, otherwise known as
47, XXY is caused by an extra X chromosome.
Edwards syndrome is caused by trisomy (three copies) of chromosome 18.
Down syndrome, a common chromosomal disease, is caused by trisomy of chromosome
21.
Patau syndrome is caused by trisomy of chromosome 13.
Also documented are trisomy 8, trisomy 9 and trisomy 16, although they generally do not
survive to birth.

Some disorders arise from loss of just a piece of one chromosome, including
Cri du chat (cry of the cat), from a truncated short arm on chromosome 5. The name
comes from the babies' distinctive cry, caused by abnormal formation of the larynx.
1p36 Deletion syndrome, from the loss of part of the short arm of chromosome 1.
Angelman syndrome – 50% of cases have a segment of the long arm of chromosome 15
missing; a deletion of the maternal genes, example of imprinting disorder.
Prader-Willi syndrome – 50% of cases have a segment of the long arm of chromosome
15 missing; a deletion of the paternal genes, example of imprinting disorder.

Chromosomal abnormalities can also occur in cancerous cells of an otherwise genetically

normal individual; one well-documented example is the Philadelphia chromosome, a
translocation mutation commonly associated with chronic myelogenous leukemia and
less often with acute lymphoblastic leukemia.