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Unusual chromosomes and their properties
Genetic material is present as chromosomes which are complex structures consisting of DNA and proteins. These chromosomes contain genes encoding for proteins which regulate the reactions in living systems. Chromosomes are small structures. In some cases, chromosomes which are larger than the normal size and different in structure are found in plants and animals.

B chromosomes are accessory or supernumerary chromosomes present in the cell as extra chromosomes over the standard complement of diploid or polyploidy chromosomes. These chromosomes are dispensable, heterochromatinized. These are non-homologous to standard chromosomes and do not follow Mendelian laws. These unusual chromosomes are considered to be genetically inactive. B chromosomes are mostly present in plants and in a less frequency in animals. Among plants about 1000 species were found to have B chromosomes including Bryophytes and family Graminae and Liliaceae. B chromosomes are said to be formed by non-disjunction of chromosomes during inter specific and intra specific crosses. According to Peters, B chromosomes are not transferred from generation to generation and produce denova. B chromosomes are classified as interspecific autosomal; inter specific sex chromosomal, intra specific autosomal and intra specific sex chromosomal. B chromosomes play a significant role in characters. Increased number of B chromosomes reduces the vigour and fertility of pollen grains and seeds. In pollen grains, the generation cell receives all the B chromosomes and out of two sperm cells one receives all the B chromosomes and this sperm cell fuses with the egg. Whereas in animal cells, B chromosomes are confined to females. B chromosomes influence flowering in plants and in Rye, the increase in number of B chromosomes to eight increase number of chiasmata leading to more variation.

Lamp brush chromosomes were first found in oocytes of amphibians. These are found in some invertebrates and all vertebrates except in mammals. At diplotene stage, the homologous chromosomes repel from each other, they are held together at points of chiasmata. Each homologous chromosome consist of a pair of sister chromatids. They are arranged parallel to each other that often produce loops that vary in number from 1-9 pairs. The extension of each loop is about 200 microns and the length is about 700 microns. It is proved that lamp brush chromosomes forming loops produce maximum RNA and proteins sufficient for further embryogenesis. Each loop is composed of double stranded DNA that is surrounded by matrix rich in RNA and proteins. The loop is thicker at some regions which represent inactive regions and thinner at some regions which is the active part. In the loop region, transcription of proteins occurs. And these loops remain as such till fertilization. After the fertilization of the egg, the loops condense to form chromomeres and the chromosomes act like normal chromosomes entering into the M phase.

Polytene chromosomes are also known as giant chromosomes which were first identified in antipodal cells of Fritillaria. As Balbiani discovered, the cells of salivary glands of third instar larvae of Drosophila contain these chromosomes and it disintegrates when the instar pupates. These chromosomes are 1800 times larger than the normal chromosomes. Polytene chromosomes consist of five radiating arms corresponding to an X chromosome, 2L arm, 2R arm and 3R arm. The short sixth arm represents the fourth chromosome that corresponds to heterochromatin and euchromatin respectively. In euchromatin region, the chromosomes are less condensed and form the active sites for genetic regulation. Often chromonema bulges to form Balbiani ring or chromosomal puff.
This chromosome has a unique characteristic of undergoing endomitosis where these replicate during S phase, but doesn’t enter into the cell cycle. In this, there is gene amplification as the DNA keeps dividing leading to production of more strands of chromonema. The chromonema are arranged side by side corresponding to each chromonema. Endomitosis leads to gene amplification which in turn increases transcription and translation. Thereby quantity of gene products formed is increased. Chromosomes in Drosophila show somatic pairing where chromosomes paired in undivided cells as in the zygotene stage of meiosis and due to endomitosis when the diameter increases in the homologous chromosomes and refuse to join in a common arm. The centromeres form a common centromere in pairs such that one was maternal origin and the other is of paternal origin.
Unusual chromosomes and their properties

Apart from other unusual chromosomes that occur „regularly“ in the nature (polytene, lamp brush and B chromosomes), there is also the fourth type of unusual chromosomes – Artificial chromosomes. As their name suggests, they are man-made, synthetic chromosomes, constructed with the intention to be used in genetic engineering on the chromosomal level (manipulation of whole chromosomes). This means that they contain fragments of target DNA inserted into the carrier chromosome, which can then be inserted into the host cell where they will be expressed along with the target DNA (very useful in cloning experiments/applications).

When comparing artificial chromosomes with other vector molecules used in genetic transformations, the major difference (and advantage) of artificial chromosomes is the size of the foreign target DNA they can contain. While other vectors (like plasmids and phages, or hybrid ones like cosmids and phagemids) can contain only up to 50 kb of foreign DNA (in the best case; the number is usually around 10 kb), artificial chromosomes can contain up to 1000 kb of target DNA. This makes them a lot better targets for cloning of larger genes, or for the creation of genomic libraries, e.g.

When we say artificial chromosomes (focusing on human artificial chromosomes), we mean exactly that – they are very similar to the normal chromosomes. In fact, when observed structurally, they are identical, because in order for the artificial chromosome to be functional, it must have all of the parts like the regular chromosomes do. These include centromeres, telomeres, protein scaffold, origin of replication, etc.

The main application of artificial chromosomes is like of any other vector molecule – it can be used to study specific DNA fragments. They can be inserted into the host cells (usually bacteria) which will propagate and the fragment of interest will be transcribed first, and then translated later on. The product in the form of protein can then be analyzed. The same process can also be used to study the gene expression of specific organisms, or to induce a new gene into the target organism. Moreover, artificial chromosomes are great for the creation of genomic libraries (since they can contain a lot more foreign DNA than the regular vector molecules), which effectively reduces the number of vectors needed to store genomic DNA of one organism.
Types of artificial chromosomes

YAC – Yeast artificial chromosome

YAC is the first artificial chromosome produced and it was the major breakthrough when compared to the previous vector molecules as it could contain up to 1000 kb of foreign DNA (which is about 20 times more than the hybrid vectors like cosmids and phagemids, and hundreds of times more than some regular plasmid vectors). As the name suggests, this chromosome was produced using the Yeast DNA.

YAC contains both parts of the chromosome and parts of the vector molecule. These include centromere, telomeres, origins of replication and selectable markers. The main problem with the YAC is the fact that it is unstable (this is the main reason why it was replaced with BAC – bacterial artificial chromosome during the Human Genome Project). However, its stability was improved to a certain degree by the group of scientists during the 1980s. They have accomplished this through the discovery of autonomously replicating sequences (ARS).

Autonomously replicating sequences are basically origins of replication which can also affect the plasmid stability. They are found in Yeast and the interesting thing about them is the fact that they don’t have to be used in every cell cycle.

Advantages and applications of YAC

One of the best applications of yeast artificial chromosome is its usage to express eukaryotic proteins. Regular bacterial plasmids or phages cannot be used as vectors for eukaryotic genes since eukaryotes possess specific posttranslational modifications not found in prokaryotes.

Moreover, since YACs can contain a lot of foreign DNA, they can be used in the creation of genomic libraries (genomic library contains the whole genome of one organism). This can be achieved in two ways: random fragmentation (which is better for the creation of gene bank) and partial restriction enzyme digestion (which is better for the creation of genome bank of an organism). Once the genomic library is generated, it should be maintained in the stable form.
Types of artificial chromosomes

BAC – Bacterial artificial chromosome

This is another popular artificial chromosome used in genetic engineering. The main difference between it and the yeast artificial chromosome is that YAC can contain up to three times more DNA, but the BAC is more stable.

This characteristic makes it the preferable choice when doing some genetic experiments like sequencing; especially since bacterial artificial chromosome can still contain a lot of DNA, up to around 300 kb), which is a lot more than regular plasmids or virus-based vectors. It was used during the genome projects, like in the case of Human Genome Project, which was started with YAC, but scientists decided to shift to BAC after the yeast artificial chromosome proved to be unstable. The basic idea behind the genome project is to have the organism’s whole sequence. This can be accomplished by sequencing the organism’s genome – amplifying it using BAC vectors (containing inserts of organism’s DNA) and PCR. The final sequence is ordered and produced using computers.

Bacterial artificial chromosome is based on the F-plasmid (fertility plasmid). This is important since F-plasmid contains parA and parB partition genes which contribute to the overall stability of the BAC, plus they partition the vector DNA to daughter cells during the cell division, resulting in even distribution of plasmid after the division.

Additional parts of the bacterial artificial chromosome are selectable markers, of course, like the ones for antibiotic resistance or blue/white selection. Also repE region, which is responsible for the replication initiator protein whose role is also to regulate the number of copies of BAC. It also contains the target sites where restriction enzymes will cut and where the DNA of interest will be inserted, and it has T7 and Sp6 regions, which are phage promoters, sites of the RNA pol binding and the initiation of transcription (RNA production).

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Unusual chromosomes and their properties00