New type of extra-chromosomal DNA discovered

Mar 09, 2012 by Lin Edwards report
DNA

(PhysOrg.com) -- A team of scientists from the University of Virginia and University of North Carolina in the US have discovered a previously unidentified type of small circular DNA molecule occurring outside the chromosomes in mouse and human cells. The circular DNA is 200-400 base pairs in length and consists of non-repeating sequences. The new type of extra-chromosomal circular DNA (eccDNA) has been dubbed microDNA. Unlike other forms of eccDNA, in microDNA the sequences of base pairs are non-repetitive and are usually found associated with particular genes. This suggests they may be produced by micro-deletions of small sections of the chromosomal DNA.

Professor Anindya Dutta and colleagues pruified DNA taken from samples of tissue and then digested away the linear DNA (which consists of millions of base pairs) to leave only circular DNA pieces, which they then sequenced using ultra-high-throughput sequencing. Circles were identified by a new bioinformatics program.

They found the size of the circles was around the same length as the DNA on a (a sub-unit of a chromosome). The small size of the circular DNA surprised them since extra-chromosomal DNA circles are larger. Their circular DNA was also dissimilar to the previously-known circles known as polydispersed DNA because the latter usually consist of repeating sequences of base pairs. Another interesting finding was that the circles are rich in the base pair GC (guanine-cytosine) with relatively little AT (adenine-thymine. The researchers repeated their experiments on other mouse tissues and on .

The team also compared the circular DNA to the linear DNA originally digested away, and they were able to match the microDNA with micro-deletions on the linear DNA. This result suggests that the DNA found in may exhibit more variation than previously thought, and the implication of this is that sequencing of the DNA in blood cells (which are the cells usually used for sequencing) may give misleading results if microdeletions have occurred in the DNA of other tissues but not in . Examples in which this might be important are in genetic seqencing for autism or schizophrenia, which could be caused by incorrect functioning of certain genes in . Many cancers are also caused by incorrect functioning of genes; in this case tumor suppressor genes, and sequencing of blood cell DNA could also give misleading results.

The researchers suggest that microDNA might be formed during replication of DNA or during DNA repair processes, but more research will be needed to identify the exact processes involved. The team will next turn to investigating cancer genomes.

The paper was published in the journal Science.

Explore further: Scientists tap trees' evolutionary databanks to discover environment adaptation strategies

More information: Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues, Science DOI: 10.1126/science.1213307

Abstract
We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200 to 400 bp long, derived from unique nonrepetitive sequence, and are enriched in the 5' untranslated regions of genes, exons, and CpG islands. Chromosomal loci that are enriched sources of microDNA in adult brain are somatically mosaic for microdeletions that appear to arise from the excision of microDNAs. Germline microdeletions identified by the “Thousand Genomes” project may also arise from the excision of microDNAs in the germline lineage. We have thus identified a new DNA entity in mammalian cells and provide evidence that their generation leaves behind deletions in different genomic loci.

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User comments : 9

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Lurker2358
1 / 5 (16) Mar 09, 2012
Being able to add and remove code as needed, or not needed, for specialized purposes is evidence of modular, intelligent design.
baudrunner
not rated yet Mar 09, 2012
That's a mere perception, Lurker. The leftover pieces are evidence that a randomly associative process links only enough DNA as required by a system conforming to specifications related to environmental and hereditary factors. Certain rules determine outcomes but these are introduced by the owners of the DNA, and some of them are pretty dumb, Lurker.
Mike_Massen
3.7 / 5 (6) Mar 09, 2012
Lurker2358 again had the creationist/religious bias:
Being able to add and remove code as needed, or not needed, for specialized purposes is evidence of modular, intelligent design.
Its helpful to be aware of the 'organic permutation space' which is approximately 10^60, within range of permutations it is very easy to see that structures arise that appear as if designed by a cohesive cognitive force but, look closely and you will see the structures all have flaws. In any case what evidence is there that any observer has the intelligence to arrive at a (static) conclusion there is any intelligent designer ?
So this so called intelligent designer isn't that intelligent and not such a good designer. Eg. Add up the vast amount of diseases & genetic malformations of all living things, especially the very short lifespan, that doesn't allow us to individually observe changes on a geological time scale !

Obviously life is the complex extension of chemistry, the permutation space is vast !
Neurons_At_Work
4.3 / 5 (6) Mar 09, 2012
Well, it's obvious to me that these are the equivalent of molecular RFID tags placed there when homosapiens were 'enhanced' by our ancient alien overlords two million years ago. They will be used to identify the pure and righteous among us when they return at the end of this year to rapture same. What?
kaasinees
0 / 5 (21) Mar 09, 2012
Well, it's obvious to me that these are the equivalent of molecular RFID tags placed there when homosapiens were 'enhanced' by our ancient alien overlords two million years ago. They will be used to identify the pure and righteous among us when they return at the end of this year to rapture same. What?

If only this would be true then there might still be hope left for our species.
mrlewish
5 / 5 (2) Mar 09, 2012
Being able to add and remove code as needed, or not needed, for specialized purposes is evidence of modular, intelligent design.


Your post proves the opposite.
Pooua
not rated yet Mar 09, 2012
I took a Biology class last semester, in which I experimented on mitochondrial DNA. I suspected that DNA might exist in more places than just the nucleus and mitochondria.
kaasinees
0.2 / 5 (22) Mar 10, 2012
I took a Biology class last semester, in which I experimented on mitochondrial DNA. I suspected that DNA might exist in more places than just the nucleus and mitochondria.

Yup, they are called viruses.
Torbjorn_Larsson_OM
5 / 5 (1) Mar 10, 2012
@ Lurker:

"evidence of modular, intelligent design."

Creationists should not comment on science.

Besides the ludicrous idea that anti-science can or wish to contribute to science, it is especially ludicrous when as here specifically described molecular trash from a wasteful, non-designed process is promoted as being for non-observed, non-described "purposes". This only tests that creationism and other religion is terribly wrong, and its ushers openly arguing insanely. Thanks but no thanks, we already knew that.

@ Pooua:

Besides micro-DNA and viruses there should be (I think in some cases are) DNA passed between cells* and DNA in other organelle remnants. At least one eukaryote has recently, independently from plasmids, endogenously accepted a cyanobacteria.

*Bacteria does this with plasmids, but I also vaguely remember DNA/RNA uptake anyway. Genes are useful, so there wouldn't be much of a selection advantage not to do it, I guess.

(As you can guess I'm no biologist.)

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