When the media speaks of decoding genomes, I think there’s an assumption that the decoding is perfect. I know I did. Turns out that this is wrong, and that the mistakes and missed DNA is remarkably consistent – and has been dubbed Dark DNA. Biologist Adam Hargreaves describes the realization and subsequent hunt for the missing matter in NewScientist (10 March 2018, paywall):
[From the sidebar] These days, sequencing is largely automated, so the process is much faster. Multiple copies of a DNA strand are first chopped up at random into small fragments – usually between 100 and 150 bases long – which are then sequenced individually before being pieced back together by computer programs that match overlapping sections. But there’s a problem. This “next-generation” sequencing is not very good at deciphering stretches of DNA dominated by just two bases, such as G and C, because this makes it hard to reassemble overlapping fragments. As a result, we may have overlooked substantial chunks of DNA in the genomes sequenced to date. My colleagues and I have dubbed this “dark DNA”.
And so?
[From the main story] But we realised it might explain why the corresponding DNA appeared to be missing – standard sequencing technology is not very good at picking up sections of DNA with high levels of G and C. So we set out to reveal the elusive DNA in a different way: using caesium chloride ultracentrifugation. This involves spinning chopped-up DNA in a highly concentrated salt solution very fast – at least 40,000 revolutions per minute – for three days so that denser fragments, like those rich in GC bases, sink to the bottom. Having separated this out, we attempted to sequence it alone.
It worked. What we found was a mutation hotspot – a region of DNA with an extraordinarily large number of mutations, many of them changes from A or T to G or C bases. Sand rat Pdx1, for example, contains more mutations than any other version of the gene we know of in the animal kingdom – resulting in a Pdx1 protein that, in just one key region that binds to DNA, has at least 15 amino acids differing from the normal version.
Ah! Not only are the “missing” DNA not easily detected by traditional methods, but they’re undergoing very fast mutations! A major piece of evolution occurring, and we couldn’t see it.
A great bit of detective work, if it holds up.
