Donnerstag, 23. Mai 2013

May 2013 Newsletter - focus on microDNA

Our May 2013 newsletter informs about the latest news in quantitative real-time PCR (qPCR and RT-qPCR), which are compiled and summarised on the 
Gene Quantification homepage. The focus of this newsletter issue is:

* New - microDNA - A new piece of genetics puzzle -
* Update - microRNA sub-domains - new papers on microRNA and mRNA integrative analysis -
* Update - microRNA sub-domains - new microRNA reviews -
* GenEx - a powerful tool for qPCR data analysis - download a free trial version -

microDNA -- A new piece of genetics puzzle
by DNA Decoding

In the beginning the big discovery was the existence of DNA and RNA. Eventually more refined experiments and better equipment revealed that RNA in particular came in many forms and functions, for example, micro RNA (miRNA) for DNA regulation or piwi-interacting RNA (piRNA) for transposon defense. So far there are 25-27 types of RNA. However, for DNA not so many types, in fact, basically two: chromosomal DNA, which is what most people think of as DNA, the DNA in the nucleus of every living cell. It comes with variants B (right handed helix twist) or A (right twist helix with 11 base pairs) and Z (left twist helix with 12 base pairs). Then there is mitochondrial DNA of the mitochondrion, the tiny enclosed organelle found in animal (eukaryote) cells. In short, the basic code storing function of DNA is in a relatively orderly format, whereas RNA the transcriber and regulator of DNA is very complex and geneticists continue to find more complications. Except that now there appears to be a new form of DNA, microDNA.
This new type of DNA is, for one thing, distinguished by existing outside the chromosome. Finding bits and pieces of DNA separated from the chromosome, in itself, isn’t too surprising. It’s a bit like finding flotsam along the shoreline; you expect some loose bits of material to be floating around in the cell. However, what scientists now call an extra-chromosomal circular DNA (eccDNA) may be something more significant.
One type of eccDNA, dubbed microDNA and recently discovered by scientists at the University of Virginia (USA) and the University of North Carolina (USA), is found in great numbers of relatively short strands (200-400 base pairs – the combinations of Guanine-Cytosine and Adenine-Thymine) in non-repeating sequences. Their finding has just been published in Science (Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues). Where these ‘pieces’ of DNA come from has not been verified, but geneticists think it could be from cutting bits of chromosomal DNA (excision), replication of short DNA sequences, or reverse transcription of certain RNA. The research tends to show that microDNA mostly comes from deletions, which would indicate they are part of the repair and maintenance process for DNA.
The big question is what – if anything – are microDNA pieces for? Do they play an active role in the repair process, or are they the result (detritus) of that process? They do seem to be associated with gene variation between different types of cells. So far the researchers have found microDNA in human and mouse cells, but it may not be universal. At this point there are more questions than answers, although the pattern in genetic discovery tends to lead from the simple toward the complex. It is possible that microDNA and other eccDNAs have an important role in the genome – or not. It’s these kinds of questions that keep geneticists on their toes.


Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues
Shibata Y, Kumar P, Layer R, Willcox S, Gagan JR, Griffith JD, Dutta A.
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
Science. 2012 336(6077): 82-86

A mechanism of gene amplification driven by small DNA fragments
Mukherjee K, Storici F.
School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America.
PLoS Genet. 2012 8(12): e1003119

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