Karyotype


A karyotype is the general appearance of the complete set of chromosomes in the cells of a species or in an individual organism, mainly including their sizes, numbers, and shapes. Karyotyping is the process by which a karyotype is discerned by determining the chromosome complement of an individual, including the number of chromosomes and any abnormalities.
File:NHGRI human male karyotype.png|thumb|Micrographic karyogram of human male using Giemsa staining
A karyogram or idiogram is a graphical depiction of a karyotype, wherein chromosomes are generally organized in pairs, ordered by size and position of centromere for chromosomes of the same size. Karyotyping generally combines light microscopy and photography in the metaphase of the cell cycle, and results in a photomicrographic karyogram. In contrast, a schematic karyogram is a designed graphic representation of a karyotype. In schematic karyograms, just one of the sister chromatids of each chromosome is generally shown for brevity, and in reality they are generally so close together that they look as one on photomicrographs as well unless the resolution is high enough to distinguish them. The study of whole sets of chromosomes is sometimes known as karyology.
Karyotypes describe the chromosome count of an organism and what these chromosomes 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. The preparation and study of karyotypes is part of cytogenetics.
The basic number of chromosomes in the somatic cells of an individual or a species is called the somatic number and is designated 2n. In the germ-line the chromosome number is n.p28 Thus, in humans 2n = 46.
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, medicine and to gather information about past evolutionary events.

Observations on karyotypes

Staining

The study of karyotypes is made possible by staining. Usually, a suitable dye, such as Giemsa, is applied after cells have been arrested during cell division by a solution of colchicine usually in metaphase or prometaphase when most condensed. In order for the Giemsa stain to adhere correctly, all chromosomal proteins must be digested and removed. For humans, white blood cells are used most frequently because they are easily induced to divide and grow in tissue culture. Sometimes observations may be made on non-dividing cells. The sex of an unborn fetus can be predicted by observation of interphase cells.

Observations

Six different characteristics of karyotypes are usually observed and compared:
  1. Differences in absolute sizes of chromosomes. Chromosomes can vary in absolute size by as much as twenty-fold between genera of the same family. For example, the legumes Lotus tenuis and Vicia faba each have six pairs of chromosomes, yet V. faba chromosomes are many times larger. These differences probably reflect different amounts of DNA duplication.
  2. Differences in the position of centromeres. These differences probably came about through translocations.
  3. Differences in relative size of chromosomes. These differences probably arose from segmental interchange of unequal lengths.
  4. Differences in basic number of chromosomes. These differences could have resulted from successive unequal translocations which removed all the essential genetic material from a chromosome, permitting its loss without penalty to the organism or through fusion. Humans have one pair fewer chromosomes than the great apes. Human chromosome 2 appears to have resulted from the fusion of two ancestral chromosomes, and many of the genes of those two original chromosomes have been translocated to other chromosomes.
  5. Differences in number and position of satellites. Satellites are small bodies attached to a chromosome by a thin thread.
  6. Differences in degree and distribution of GC content. In metaphase where the karyotype is typically studied, all DNA is condensed, but most of the time, DNA with a high GC content is usually less condensed, that is, it tends to appear as euchromatin rather than heterochromatin. GC rich DNA tends to contain more coding DNA and be more transcriptionally active. GC rich DNA is lighter on Giemsa staining. Euchromatin regions contain larger amounts of Guanine-Cytosine pairs. The staining technique using Giemsa staining is called G banding and therefore produces the typical "G-Bands".
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:
  1. between the sexes,
  2. between the germ-line and soma,
  3. between members of a population,
  4. in geographic specialization, and
  5. in mosaics or otherwise abnormal individuals.

    Human karyogram

Both the micrographic and schematic karyograms shown in this section have a standard chromosome layout, and display darker and lighter regions as seen on G banding, which is the appearance of the chromosomes after treatment with trypsin and staining with Giemsa stain. Compared to darker regions, the lighter regions are generally more transcriptionally active, with a greater ratio of coding DNA versus non-coding DNA, and a higher GC content.
Both the micrographic and schematic karyograms show the normal human diploid karyotype, which is the typical composition of the genome within a normal cell of the human body, and which contains 22 pairs of autosomal chromosomes and one pair of sex chromosomes. A major exception to diploidy in humans is gametes which are haploid with 23 unpaired chromosomes, and this ploidy is not shown in these karyograms. The micrographic karyogram is converted into grayscale, whereas the schematic karyogram shows the purple hue as typically seen on Giemsa stain.
The schematic karyogram in this section is a graphical representation of the idealized karyotype. For each chromosome pair, the scale to the left shows the length in terms of million base pairs, and the scale to the right shows the designations of the bands and sub-bands. Such bands and sub-bands are used by the International System for Human Cytogenomic Nomenclature to describe locations of [|chromosome abnormalities]. Each row of chromosomes is vertically aligned at centromere level.

Human chromosome groups

Based on the karyogram characteristics of size, position of the centromere and sometimes the presence of a chromosomal satellite, the human chromosomes are classified into the following groups:
GroupChromosomesFeatures
A1–3Large, metacentric or submetacentric
B4-5Large, submetacentric
C6–12, XMedium-sized, submetacentric
D13–15Medium-sized, acrocentric, with satellite
E16–18Small, metacentric or submetacentric
F19–20Very small, metacentric
G21–22, YVery small, acrocentric

Alternatively, the human genome can be classified as follows, based on pairing, sex differences, as well as location within the cell nucleus versus inside mitochondria:
  • 22 homologous autosomal chromosome pairs. Homologous means that they have the same genes in the same loci, and autosomal means that they are not sex chromomes.
  • Two sex chromosome : The most common karyotypes for females contain two X chromosomes and are denoted 46,XX; males usually have both an X and a Y chromosome denoted 46,XY. However, approximately 0.018% percent of humans are intersex, sometimes due to variations in sex chromosomes.
  • The human mitochondrial genome, although this is not included in micrographic karyograms in clinical practice. Its genome is relatively tiny compared to the rest.

    Copy number

Schematic karyograms generally display a DNA copy number corresponding to the G0 phase of the cellular state which is the most common state of cells. The schematic karyogram in this section also shows this state. In this state, each cell has two autosomal chromosomes of each kind, where each chromosome has one copy of each locus, making a total copy number of two for each locus. At top center in the schematic karyogram, it also shows the chromosome 3 pair after having undergone DNA synthesis, occurring in the S phase of the cell cycle. This interval includes the G2 phase and metaphase. During this interval, there is still 2n, but each chromosome will have two copies of each locus, wherein each sister chromatid is connected at the centromere, for a total of 4c. The chromosomes on micrographic karyograms are in this state as well, because they are generally micrographed in metaphase, but during this phase the two copies of each chromosome are so close to each other that they appear as one unless the image resolution is high enough to distinguish them. In reality, during the G0 and G1 phases, nuclear DNA is dispersed as chromatin and does not show visually distinguishable chromosomes even on micrography.
The copy number of the human mitochondrial genome per human cell varies from 0 up to 1,500,000, mainly depending on the number of mitochondria per cell.

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:
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.