Chromosome Banding

What is Chromosome Banding. Let us know about chromosome banding. Karyotyping is the process by which chromosomes are photographed to determine an individual’s chromosome complement , which includes the number of chromosomes and any abnormalities. The term karyotype is also used for the entire set of chromosomes in a species or in an individual organism and for a test that detects or measures this complement.

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

The study of the entire set of chromosomes is sometimes referred to as karyology . Chromosomes are depicted (by rearranging a microscope photograph) in a standard format known as a karyogram or idiogram : in pairs, ordered by size and position of the centromere for chromosomes of the same size.

The basic number of chromosomes in the somatic cells of an individual or species is called the somatic number and is designated 2n . In the germ-line (sex cells) the chromosome number is n (humans: n = 23). [2] p28 Thus, 2n = 46 in humans .

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 studying chromosomal aberrations , cellular function, taxonomic relationships, medicine , and gathering information about past evolutionary events ( karyosystematics ).

History of Karyotype Studies

Chromosomes are first observed in plant cells. Their behavior in animal ( salamander ) cells was described by Walther Fleming , the inventor of mitosis , in 1882. Another German anatomy, the name was coined by Carl Wilhelm von Ngeli in 1842. Heinrich von Waldeyer in 1888 it is New Latin from Ancient Greek karyon , “kernel”, “seed,” or “nucleus”, and typos , “normal form”)

Joe Hin Tjio, working in Albert Levan’s laboratory ^{[14] found that the number of chromosomes was 46 using new techniques available at the time:}

1. Using Cells in Tissue Culture
2. pre-treating cells in a hypotonic solution, which causes them to swell and stretch the chromosomes
3. A solution of metaphase arrest in mitosis by colchicine
4. Crush the preparation on the slide to force the chromosomes into a single plane.
5. Cutting a photomicrograph and arranging the result into an undistorted workogram.

The work took place in 1955, and was published in 1956. The karyotype of humans consists of only 46 chromosomes. ^[15] [16] Other great apes have 48 chromosomes. Human chromosome 2 is now known to be the result of end-to-end fusion of two ancestral ape chromosomes. 

Overview of Karyotype

Getting obscured

The study of karyotype is made possible by staining. Typically, a suitable dye, such as Giemsa, is applied after ^{[19] cells have been arrested during cell division by resolving 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 most often used because they are readily induced to divide and grow in tissue culture. ^[20] Sometimes observations can 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 bar body). (Chromosome Banding)

Comments

Six different characteristics of the karyotype are commonly observed and compared: ^[21]

1. The difference in the absolute size of the chromosomes. Chromosomes can vary up to twenty-fold in absolute size 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. The difference in the position of the centromere. These differences probably came about through translation.
3. The difference in the relative size of the chromosomes. These differences probably arose from segmental exchanges of unequal length.
4. The difference in the original number of chromosomes. These differences can result from frequent unequal translocations, which remove all necessary genetic material from a chromosome, allowing the organism to lose it without penalty (dislocation hypothesis) or through fusion. Humans have one pair less chromosomes than great apes. Human chromosome 2 appears to have resulted from the fusion of two paternal chromosomes, and that many of the genes from those two parent chromosomes have been transferred to other chromosomes.
5. The difference in the number and position of satellites. Satellites are small bodies attached to a chromosome by a thin thread.
6. Differences in the degree and distribution of heterogeneous areas. Heterochromatin stains darker than euchromatin. Heterochromatin is more tightly packed. Heterochromatin mainly consists of genetically inactive and repetitive DNA sequences as well as a large amount of adenine-thymine pairs. Euchromatin is usually under active transcription and is very lightly stained because it has low affinity for the JIMSA stain. ^[22] Euchromatin regions contain large amounts of guanine–cytosine pairs. The staining technique using Giemsa staining is called G-banding and therefore produces the distinctive “G-band”. ^[22]

Therefore a complete account of the karyotype may include the number, type, size and banding of chromosomes as well as other cytogenetic information.

Variation is often found:

1. between the sexes,
2. between the germ line and the soma (between the gamete and the rest of the body),
3. between members of a population (chromosomal polymorphisms),
4. geographic expertise in, and
5. In mosaics or otherwise unusual individuals. ^[9]

Human karyotype

The typical human karyotype consists of 22 pairs of autosomal chromosomes and one pair of sex chromosomes (allosomes). The most common karyotype for females has two X chromosomes and is denoted 46,XX; Males usually have both an X and a Y chromosome indicating 46,XY. About 1.7% percent of humans are intersex, sometimes due to variation in sex chromosomes. ^{[23] [24] [ unreliable source ]}

Certain variations in karyotype, whether autosomes or allosomes, cause developmental abnormalities.

Karyotype diversity and evolution

Although the DNA of replication and transcription was highly standardized in eukaryotes, the same cannot be said for their karyotypes, which are highly variable. Despite their construction from the same macromolecules, chromosome numbers and detailed organization vary between species. This variation provides the basis for a range of studies in evolutionary cytology.

In some cases there is significant variation even within species. In a review, Godfrey and Masters concluded:

In our view, it is unlikely that one process or the other could be responsible for the wide range of independently observed karyotype structures… but, used in conjunction with other phylogenetic data, karyotypic fragmentation into diploid Might help explain the dramatic difference in numbers. Among closely related species, which were previously inexplicable. ^[25]

Although much is known about karyotypes at the descriptive level, and it is clear that changes in karyotype organization have had an impact on the evolutionary course of many species, it is not exactly clear what general significance may be.

Despite many careful investigations, we have a very poor understanding of the causes of karyotype evolution… The general significance of karyotype evolution remains unclear.

Change during development

Instead of general gene repression, some organisms go for massive elimination of heterochromatin, or other types of visual adjustment of karyotype. (Chromosome Banding)

• Chromosome elimination. In some species, as in many syarid flies, entire chromosome ends are lost during development. ^[27]
• Chromatin degradation (Founding Father: Theodore Boveri). In this process, as found in some copepods and roundworms such as Ascaris sumac , parts of the chromosomes are moved away into specialized cells. This process is a carefully arranged genome rearrangement where new telomeres are created and some heterochromatin regions are lost. ^[28] [29] In A suum , all somatic cells undergo preceding chromatin reduction. ^[30]
• X-inactivation. Inactivation of an X chromosome occurs during early development of mammals (see Barr body and dosage compensation). In placental mammals, inactivation is as random between the two Xs, thus the mammalian female is a mosaic with respect to her X chromosomes. In marsupial it is always the parental X which is deactivated. Some 15% of somatic cells in human females survive inactivation, ^[31] and the number of affected genes on the inactive X chromosome varies between cells: in fibroblast cells about 25% of the genes on the Barr body survive inactivation. ^[32]

Number of chromosomes in a set

A striking example of variability among closely related species is the muntjac, which was investigated by Kurt Benirschke and Doris Wurster. The diploid number of the Chinese muntjac, Muntiacus reevesi , was found to be 46, all farsighted. When they looked at the karyotype of the closely related Indian muntjac, Muntiacus muntjac , they were surprised to find that it had female = 6, male = 7 chromosomes. ^[33]

They couldn’t 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 got some more samples they confirmed [their findings] .

The number of chromosomes in a karyotype is extremely variable between (relatively) unrelated species. The following record is held by the nematode Parascaris univalents , where haploid n = 1; and an ant: Myrmacea pilosula . ^[34] The record high would be somewhere between ferns, with the adder’s tongue fern ophioglossum leading the way with an average of 1262 chromosomes. ^{[35] The top score for the animal may be the shortnose sturgeon} acipensor brevirostrum on 372 chromosomes . ^[36]The existence of supernumerary or B chromosomes means that chromosome numbers can vary even within an interbreeding population; And aneuploids are another example, although in this case they would not be considered as normal members of the population. (Chromosome Banding)

Fundamental number

The fundamental number of the karyotype, Fn , is the number of visible major chromosome arms per set of chromosomes. ^[37] [38] Thus, Fn 2 x 2n differentiate based on the number of chromosomes considered single-armed (acrocentric or telocentric). ^{Humans have Fn = 82, [39]} due to the presence of five acrocentric chromosome pairs : 13, 14, 15, 21, and 22 (the human Y chromosome is also acrocentric). The fundamental autosomal number or autosomal elemental number, FNA ^[40] or AN , ^[41] is the number of visible major chromosomal arms per set of autosomes (non-gender-linked chromosomes) of a karyotype.

Ploidy

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

• Polyploidy, where cells have more than two sets of homologous chromosomes, occurs mainly in plants. According to Stebbins, it has been of major importance in the development of plants. ^{[42] [43] [44] [45]} The proportion of flowering plants that are polyploid was estimated by Stebbins to be 30–35%, but grasses average much higher, around 70%. ^[46] Polyploidy in lower plants (ferns, horsetails and psilotales) is also common, and some species of ferns have reached levels of polyploidy far higher than the highest known levels in flowering plants.

Polyploidy is much less common in animals, but has been significant in some groups. ^[47]

Polyploid chains in related species that consist entirely of multiples of an original number are known as euploids.

• Haplo-diploidy, where one sex is diploid, and the other is haploid. This is a common arrangement in Hymenoptera and some other groups.
• Endopolyploidy occurs when cells of differentiated tissue in the adult have ceased to divide by mitosis, but the nucleus contains a higher number of somatic chromosomes than the original. ^[48] ​​In the endocycle (endomitosis or endoreduplication) chromosomes in a ‘resting’ nucleus undergo duplication, separating daughter chromosomes from each other inside an intact nuclear membrane. ^{[49] In}
  many instances, the endopolyploid nucleus contains thousands of chromosomes (which cannot be accurately counted). Cells do not always have exact multiples (powers of two), which is why the simple definition ‘increased number of chromosome sets due to replication without cell division’ is not quite accurate.
  This process (particularly studied in insects and some higher plants such as maize) may be an evolutionary strategy to increase the productivity of tissues highly active in biosynthesis. ^[50]
  This phenomenon occurs sporadically throughout the eukaryote kingdom, from protozoa to humans; It is diverse and complex, and functions in differentiation and morphogenesis in many ways. ^[51]
• For an investigation of ancient karyotype duplication see Paleopolyploidy.

Aneuploidy

Aneuploidy is the condition in which the chromosome number in the cells is not the number specific to the species. This will lead to a chromosomal abnormality such as an extra chromosome or one or more chromosomes being lost. Abnormalities in chromosome number usually cause defects in development. Examples are Down syndrome and Turner syndrome.

Aeuploidy can also occur within a group of closely related species. Classic examples in plants are the genus Crepis , where gamete (=haploid) numbers form the series x = 3, 4, 5, 6 and 7; and crocus , where each number from x = 3 to x = 15 is represented by at least one species. Various types of evidence suggest that development trends have gone in different directions in different groups. ^[52] In primates, great apes have 24×2 chromosomes while humans have 23×2. Human chromosome 2 was formed by the merger of paternal chromosomes, reducing the number. ^[53]

Chromosomal polymorphism

Some species are polymorphic for different chromosomal structural variants. ^[54] Structural variation may be associated with different numbers of chromosomes in different individuals, which occurs in the ladybird beetle Chilocorus stigma , some mantids of the genus Ameles , ^{[ citation needed ]} the European shrew Sorex Araneus . ^[55] There is some evidence, from the case of the mollusk Thys lapillus on the Brittany coast , that the two chromosomal forms are adapted to different habitats. ^[56]

Species tree

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 L. Carson.

At approximately 6,500 square miles (17,000 km ⁾ , the Hawaiian Islands have the most diverse collection of drosophilid flies in the world, living from rainforests to sub-grasslands. These roughly 800 aerial 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 on the evolutionary tree long before genome analysis became practical. In a sense, the gene arrangement is reflected in the banding pattern of each chromosome. Chromosome rearrangements, especially inversions, make it possible to see which species are closely related.

The results are clear. The inverses, when plotted in tree form (and independent of all other information), show a clear “flow” of island species from old to new. There have also been cases of colonization and island abandonment on older islands, but these are much less frequent. Using K-Ar dating, the present-day islands date from 0.4 million years ago (mya) (Mauna Kea) to 10mya (Neckar). Still above the sea is the oldest member of the Hawaiian archipelago, Kure Atoll, which may be dated to 30 mya. The archipelago itself (moving over a hot spot by the Pacific Plate) has existed for a long time, at least in the Cretaceous. The last islands now form the Emperor Seamount Chain under the sea (mayots). 

All native Drosophila and Scaptomyza species in Hawaii are clearly descended from a single ancestral species that probably colonized the islands 20 million years ago. Subsequent adaptive radiation was driven by a lack of competition and a variety of niches. But while it would be possible for a single pregnant female to colonize an island, it is more likely that there has been a group from the same species. 

There are other animals and plants on the Hawaiian archipelago that have undergone similar, if less spectacular, adaptive radiations. ^[62] [63]

Chromosome banding

Chromosomes display a banded pattern when treated with certain stains. The bands are alternating light and dark stripes that appear along the length of the chromosomes. Unique banding patterns are used to identify chromosomes and diagnose chromosomal aberrations, including chromosome breakage, loss, duplication, translocation, or inverted segments. A range of different chromosome treatments produce a range of banding patterns: G-band, R-band, C-band, Ku-band, T-band and NOR-band.

karyotype illustration

Types of banding

Cytogenetics employs several techniques to visualize different aspects of chromosomes: ^[20]

• G-banding is obtained with Giemsa stain after digestion of chromosomes with trypsin. This generates a series of light and dark stained bands – dark regions are heterochromatic, late replication and AT rich. The light regions are euchromatic, early-replicating and GC rich. This method will typically produce 300-400 bands in a normal, human genome.
• R-banding is the opposite of G-banding (R stands for “reverse”). Dark regions are euchromatic (guanine–cytosine rich regions) and bright regions are heterochromatic (thymine–adenine rich regions).
• C-banding: Giemsa constitutes heterochromatin, so it stains the centromere. The name is derived from centromeric or constitutive heterochromatin. Prior to staining the preparation undergoes alkaline denaturation leading to almost complete degradation of DNA. After washing the probe the remaining DNA is resuspended and stained with Giemsa solution consisting of methylene azure, methylene violet, methylene blue and eosin. Heterochromatin binds a lot of the dye, while the rest of the chromosomes absorb very little of it. C-bonding proved to be particularly suitable for the characterization of plant chromosomes.
• Q-banding is a fluorescent pattern obtained by using quinacrine for staining. The pattern of the band is the same as that of G-banding. They can be recognized by yellow fluorescence of varying intensity. The majority of stained DNA is heterochromatin. Quinacrine (atebrin) binds to both regions rich in AT and GC, but only the AT-quinacrine-complex fluoresces. Since regions enriched in AT are more common in heterochromatin than in euchromatin, these regions are preferentially labeled. Different intensities of a single band reflect different contents of AT. Other fluorochromes such as DAPI or Hoechst 33258 also lead to characteristic, reproducible patterns. Each of them produces its own distinctive pattern. In other words: The properties of the bonds and the specificity of the fluorochromes are not based exclusively on their affinity for regions rich in AT. Rather, the distribution of AT and the association of AT with other molecules such as histones, for example, affect the binding properties of fluorochromes.
• T-Banding: Visualize Telomeres.
• Silver Staining: Silver nitrate stains nuclear organization region-associated proteins. This produces a dark area where silver accumulates, indicating the activity of rRNA genes within the NOR.

Classic Karyotype Cytogenetics

In the “classic” (pictured) karyotype, the dye, often Giemsa (G-banding) , less often mepacrine (quinacrine), is used to stain bands on chromosomes. Giemsa is specific for the phosphate groups of DNA. Quinacrine binds to adenine-thymine-containing regions. Each chromosome has a distinctive banding pattern that helps identify them; The banding pattern of both chromosomes in a pair will be the same.

Karyotypes are arranged with the short arm of the chromosome at the top and the long arm at the bottom. Some karyotypes have short and long arms called p and q respectively . In addition, different stained regions and subregions are assigned 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 the deletion of p15.2 (locus on chromosome), which is written as 46,XX,del(5)(p15.2). ^[64]

Multicolor FISH (mFISH) and Spectral Karyotype (SKY Technique)

Multicolor FISH and older spectral karyotyping are molecular cytogenetic techniques used to simultaneously visualize all pairs of chromosomes in an organism in different colours. Fluorescently labeled probes for each chromosome are made by labeling chromosome-specific DNA with different fluorophores. Since there is a finite number of spectrally different fluorophores, a combination labeling method is used to generate the many different colors. Fluorophore combinations are captured and analyzed by a fluorescence microscope using 7 narrow-banded fluorescence filters, or, in the case of spectral karyotyping, using an interferometer attached to a fluorescence microscope. In the case of an mFISH image, Each combination of fluorochromes from the resulting original images is replaced with a pseudocolor in a dedicated image analysis software. Thus, chromosomes or chromosome classes can be visualized and identified, allowing analysis of chromosomal rearrangements.^[65] In the case of spectral karyotyping, image processing software assigns a pseudo-colour to each spectral distinct combination, allowing visualization of the individually colored chromosomes.

Multicolor FISH is used to identify structural chromosomal aberrations in cancer cells and other pathological conditions when Giemsa banding or other techniques are not accurate enough.

Digital karyotyping

Digital karyotyping is a technique used to measure DNA copy number on a genomic scale. Short sequences of DNA from specific loci throughout the genome are isolated and enumerated. ^[67] This method is also known as virtual karyotyping.

Chromosomal abnormalities

Chromosome abnormalities can be numerical, such as in the presence of extra or missing chromosomes, or structural, such as derived chromosomes, translocations, inversions, mass deletions or duplications. Numerical abnormalities, also known as aneuploidy, often result from non-disjunction in the formation of a gamete during meiosis; Trisomy, in which three copies of a chromosome are present instead of the usual two, are common numerical abnormalities. Structural abnormalities often result from errors in homologous recombination. Both types of abnormalities can occur in gametes and therefore will be present in all cells in the body of the affected individual, or they can occur during mitosis and give rise to a genetic mosaic individual consisting of some normal and some abnormal cells.

In humans

Chromosomal abnormalities that cause disease in humans include:

• Turner syndrome results from a single X chromosome (45, X or 45, X 0).
• Klinefelter syndrome, the most common male chromosome disease, otherwise known as 47,XXY, is caused by an extra X chromosome.
• Edwards syndrome is caused by trisomy (triple copy) 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.
• Trisomy 9, which is considered the fourth most common trisomy, has many long-term affected individuals, but only in forms other than a complete trisomy, such as trisomy 9p syndrome or mosaic trisomy 9. They often work quite well, but they do have trouble. with speech.
• Trisomy 8 and trisomy 16 are also documented, although they usually do not survive until birth.

Some disorders result from the loss of only one piece of a chromosome, including

• Cri du chat (cat’s cry), from a small short arm on chromosome 5. The name comes from the characteristic crying of babies, caused by an abnormal formation of the larynx.
• 1p36 deletion syndrome, characterized by loss of part of the short arm of chromosome 1.
• Angelman syndrome – a segment of the long arm of chromosome 15 is missing in 50% of cases; Deletion of maternal gene, example of imprinting disorder.
• Prader-Willi syndrome – a segment of the long arm of chromosome 15 is missing in 50% of cases; Deletion of an ancestral gene, example of imprinting disorder.
• Cancer cells of an otherwise genetically normal person may also have chromosomal abnormalities; A well-documented example is the Philadelphia chromosome, a translocation mutation most commonly associated with chronic myelogenous leukemia and less often with acute lymphoblastic leukemia.