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I specify eukaryote in the title, but I'm also interested if this question isn't applicable to eukaryote cells in general but is to humans. I was reading "RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays" (John Marioni 2008).

In the results it states

"By these criteria, 40% of reads mapped uniquely to a genomic location, and of these, 65% mapped to autosomal or sex chromosomes (the remainder mapped almost exclusively to mitochondrial DNA)."

I couldn't help but notice the "almost exclusively to mitochondrial DNA". Almost exclusively? Can DNA be found in places other than chromosones or mitochondria? Perhaps I'm interpreting the sentence wrong. Any pointers would be appreciated

Thanks

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In plants, chloroplasts and other plastids contain DNA, but I suppose you are more interested in humans. Quoting from wikipedia,

In many cells cytoplasmic DNA is also found, which is different from nuclear DNA, both in methylation levels (cytoplasmic has less), and in sequence. EccDNA or extrachromosomal circular DNA is present in all eukaryotic cells, derived from genomic DNA and consists of repetitive sequences of DNA found in both coding and non-coding regions of chromosomes. EccDNA can vary in size from less than 2000 more than 20,000 base pairs. In animals, eccDNA molecules have been shown to contain repetitive sequences that are seen in satellite DNA, 5S ribosomal DNA and telomere DNA. The function of eccDNA has not been widely studied, but it has been proposed that the production of elements of eccDNA from genomic DNA sequences adds to the plasticity of the eukaryotic genome and can influence genome stability, cell aging and the evolution of chromosomes

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    $\begingroup$ You should 'quote' with reference if you are copy pasting from external source. $\endgroup$
    – Dexter
    Nov 6 '15 at 13:58
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    $\begingroup$ I'm sorry! I'm new to Biology SE, and will keep that in mind while answering future questions. $\endgroup$
    – Malhar Khushu
    Nov 6 '15 at 14:03
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    $\begingroup$ Sure, no problem. It is not just for SE, in general in science you should practice that :) $\endgroup$
    – Dexter
    Nov 6 '15 at 14:08
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In some reference genomes, D. melanogaster comes to mind, there are chromosomes designated as 'U' that contain sequenced genomic contigs of nuclear DNA that have not been physically mapped to one of the genetic linkage maps, or cytogenetic chromosomes.

These segments are probably flanked by long regions of repetitive DNA, and the sequencing techniques cannot unambiguously link these contigs up to the other huge contigs.

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  • $\begingroup$ That is true, but this is still in the nucleus. The question was about DNA in the cytosol. $\endgroup$
    – JereB
    Nov 6 '15 at 20:27

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