Field of Science

Some more junk DNA shown to have function

ResearchBlogging.orgHere's another study that's going to get creationist arms in the air. It shows a function for some "junk DNA" - DNA that does not serve any function for the developing organisms - namely in coding for micropeptides (very short proteins), which have now been shown to have a regulatory function in Drosophila. The first lines of the abstract reads
A substantial proportion of eukaryotic transcripts are considered to be noncoding RNAs because they contain only short open reading frames (sORFs). Recent findings suggest, however, that some sORFs encode small bioactive peptides. Here, we show that peptides of 11 to 32 amino acids encoded by the polished rice (pri) sORF gene control epidermal differentiation in Drosophila by modifying the transcription factor Shavenbaby (Svb). [Emphasis added.]
It's actually quite interesting, the finding that very short proteins have a regulatory effect on gene expression, much the same way that very short RNA molecules do (microRNA). But it doesn't mean that all DNA has a function. Just some more than what we previously thought. Some.

Of course, the researchers have not shown that all DNA has a function, which is nevertheless how this is going to be presented, tacitly. For example:
But according to David Stern, a Princeton professor in the Department of Ecology and Evolutionary Biology, scientists increasingly believe "junk DNA" is crucial for turning the information encoded in genes into useful products.

For those who think that no DNA is without function, please consider The Onion Test.
The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?
An inordinate fondness for beetles, and also for very large and redundant genomes, perhaps?

Kondo, T., Plaza, S., Zanet, J., Benrabah, E., Valenti, P., Hashimoto, Y., Kobayashi, S., Payre, F., & Kageyama, Y. (2010). Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis Science, 329 (5989), 336-339 DOI: 10.1126/science.1188158

Update 7/19:

This table shows the genome sizes for 30 species of onions. They all have huge genomes (from Evolution of genome size across some cultivated Allium species, A. Ricroch, R. Yockteng, S.C. Brown, and S. Nadot, Genome 48: 511–520, 2005).

Click for larger image.


  1. Allium fur allesJuly 19, 2010 2:12 PM

    re: Onion test...
    Ohions taste great. Non-coding DNA also tasts great (if it didn't, onions would have a tough time tasting so great). Ipso facto, all DNA has value (at the very least it tastes great).

    But I might be wrong. There, I said it.

  2. Allium fur allesJuly 19, 2010 2:14 PM

    Wrong and poor at spelling...

    And I have no idea how Ohions taste, perhaps like Onions??

  3. Allium, you are right, of course, that onions taste great. However, taking them seriously, for just a second, let me say that...

    It is unlikely that onions (and the many other species with huge genomes) required their huge genomes because non-coding DNA tastes great, because most species actually do what they can to avoid being tasty, because being eaten is such a disadvantageous thing for an organism. That said, this does not apply to species whose method of reproduction involves being eaten, such as fruits with seeds. However, onions are not one of those.

    Personally, I prefer coding DNA, but I know people who prefer non-coding.

  4. Allium fur allesJuly 19, 2010 3:21 PM

    Oh be careful now Grasshopper...

    There is a list (albiet a relatively short list) of organisms who have made a pretty fair go of it EXACTLY by being tasty. But there is a qualification. It matters most whom you are tasty to. Tasty to Homo sapiens can get you into the Domesticate class. This is a special class. These H. sapiens guys will take good care of you, select among your progeny for ability to grow in vast and varied environs, spread your progeny around the planet, and even modify the natural environment just so that it suits you better.

    Onions belong in this domesticate class, along with strawberries (check out the genome organization of a strawberry - a real head scratcher) and all those other fruits, vegetables, cereals, legumes (and this is only those boring plant members). The common bread wheat that H. sapiens has been in love with for millenia is a real genomic Frankenstein. But you find it growing all over the planet.

    So being tasty isn't always a bad thing - just choose your partners carefully.

  5. Yeah yeah, but only in the case of farming by humans is this true. The question is when the huge genomes of onions evolved.

    Amphiuma means probably does not owe it's huge genome to human cultivation, because all Allium species have huge genomes (see newly added image in main post).

  6. Allium fur allesJuly 19, 2010 5:18 PM

    Whole genome duplication may not occur in direct response to human cultivation. However there may be value to us that is therefore maintained by us. Following genome duplications there can be losses of DNA (in plants at least - I know far too little about animals). But if a domestication takes place and we find a certain type to be useful (and we learn to propagate the beast... which sort of goes hand in hand with the domestication) then other selection pressures in nature can be overridden by what we deem necessary.

    There is some evidence that seed size in soybean may be related to DNA content. Let me dig up a reference or two. Seed size in soybean is, BTW, a domesticating criteria... the wild soybean has a pretty tiny seed. Our Asian ancestors found long ago (>3,000 years ago) that some soybean types had larger seed and could be deliberately cultivated (and used for many different foods). Now soybean is grown on more than 150 million acres of the earth every year. That sounds like a fitness success to me. (and perhaps why onions make us cry??)

  7. Allium fur allesJuly 19, 2010 5:25 PM

    Relationships between nuclear DNA content and seed and leaf size in soybean

    Chung, et al. TAG 96, 1064-1068 (1998)

    The abstract is freely available at Springer. If you would a reprint, let me know. I know a couple of the authors.

  8. Still, it remains to be shown that big genomes makes for tastier (or is some other way better) crops. And then there's the fact that non-cultivated species also have big ones, which at least shoots down the idea that genome size is necessarily linked to cultivation.

  9. Allium fur allesJuly 20, 2010 4:30 AM

    "Necessarily linked" is a fair standard to ask for in our pursuit of understanding this phenomenon of giant genomes. And I'm not going to suggest that cultivation *causes* genome size increase - or that larger more complex genomes predispose H. sapiens to take an organism 'under the wing' and start cultivating it. But we humans do benefited from the phenotypic plasticity of our domesticate partners. And it seems at least somewhat possible that increased phenotypic plasticity may be one potential benefit for carrying such a large amount of DNA.

    Between the plant and animal kingdoms there is an enormous gap in tolerance to polyploidy. Plants don't seem to mind so much and in general animals react quite severely to having their chromosome numbers messed with.

    So I think we should enjoy the flavor of our Allium buddies while we keep looking at this phenomenon of giant genomes and see if we can't figure out what all this extra DNA is up to.


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