Tuesday, 24 April 2012

Extrachromosomal ‘MicroDNA’ provides an insight into genotypic mutation Denver Khoo (42907284)


Extrachromosomal DNA (DNA located separately from the chromosomes) is an established component of cell biology and can be observed in mitochondria, chloroplasts and bacterial plasmids.  Scientists from the University of Virginia and University of North Carolina have recently found a new form of circular extrachromosomal DNA, dubbed microDNA, in mouse and human cells. 



Figure 1: Multiple Displacement Amplification process (Fechner & McGovern, 2011)

An exonuclease enzyme was used to digest away the linear DNA, allowing the remaining circular DNA to be enriched through multiple displacement amplification (MDA).  As the name implies, the MDA process amplifies the small amount of sample material available similar.  It occurs in three phases as shown in Figure 1.  First, the bonding of primers to the sample DNA template, followed by DNA synthesis carried out by ɸ29 DNA polymerase.  When DNA synthesis reaches the next primer, the newly formed strand is displaced and functions as a new template shown by stages 4, 5 and 6 (Tindall & Kunkel, 1988).  In this way, tens of thousands of microDNA rings were identified and found in regions responsible for the coding and control of genetic information.

Figure 2: MicroDNA Rings (Shibata, et al., 2012)
In contrast to the repetitive sequence of common extrachromosomal DNA, microDNA rings were considerably smaller, about 200-400 base pairs in length, and derived from a “unique non-repetitive sequence” (Wilson & Williamson, 1997) (Shibata, et al., 2012).  The study found that chromosomal loci with an abundance of microDNA were found to be “somatically mosaic for microdeletions” (Shibata, et al., 2012).  Basically, this means that portions of microDNA were able to be matched with microdeletions on the original DNA strands by their “GC composition, length distribution and AA/AT/TT periodicity” (Shibata, et al., 2012).  

This suggests a potential explanation for genetic mutation and variation in somatic cells.  Since microdeletions appear to occur at random, it is plausible for some cells to have a deletion on gene 1, for example, while other cells have a deletion on gene 2.  Thus, any given tissue may possess cells with slightly different genetic material.  Despite an extensive array of proof-reading and repair mechanisms, the discovery of microDNA suggests that “occasionally DNA replication is sloppy” (Lang, 2012).         
Figure 3: Microdeletion on DNA strand (Mirmillon, 2005)
These microdeletions often have no impact on gene expression, however cell function may potentially be impaired or even prevented by chance occurrences of microdeletions in important chromosomes.  A safeguard against this usually exists since two copies of a gene are present in every cell (from the mother and father); however, issues may arise if one copy has a mutation while the other possesses a microdeletion.  This could explain the source of an array of illnesses, for example tumour suppressing genes with an incorrect DNA sequence may be rendered useless in cancer protection.  Alternatively, given that a large proportion of microdeletions were found in the brain of mouse embryos it is possible that human cases of “schizophrenia and autism...may be due to incorrect functioning of certain genes in brain tissue” (Shibata, et al., 2012) (Lang, 2012). 


Evidently, the results collected by researchers from the Universities of Virginia and North Carolina elucidate the mechanisms of genotypic mutation and variation.  Furthermore, the discovery of microDNA lends itself to the investigation of the origins of genetic disorders which may be prevented if additional research reveals a method of inhibiting DNA microdeletions.






Reference List
Edwards, L., 2012. New type of extra-chromosomal DNA discovered. [Online]
Available at: http://www.physorg.com/news/2012-03-extra-chromosomal-dna.html
[Accessed 15 March 2012].
Lang, L., 2012. Small DNA circles found outside the chromosomes in mammalian cells and tissues, including human cells. [Online]
Available at: http://www.physorg.com/news/2012-03-small-dna-circles-chromosomes-mammalian.html
[Accessed 15 Marth 2012].
Lang, L., 2012. Small DNA circles found outside the chromosomes in mammalian cells and tissues, including human cells. [Online]
Available at: http://www.physorg.com/news/2012-03-small-dna-circles-chromosomes-mammalian.html
[Accessed 15 March 2012].
Shibata, Y. et al., 2012. Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues. Science, pp. 1-5.
Tindall, K. R. & Kunkel, T. A., 1988. Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry, 27(16), pp. 6008-6013.
Wilson, R. J. & Williamson, D. H., 1997. Extrachromosomal DNA in the Apicomplexa. Microbiology and Molecular Biology Reviews, Volume 61, pp. 1-16.

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