Non-coding DNA and the opossum genome.

The genome sequence of the gray short-tailed opossum, Monodelphis domestica, was published in today’s issue of Nature (Mikkelsen et al. 2007). It is interesting for many reasons, including its status as the first marsupial genome to be sequenced, its relatively large genome size, and low chromosome number (2n = 18). It is also interesting because it contains a similar number of genes (18,000 – 20,000) to humans, the vast majority of which exhibit close associations with the genes of placental mammals. Also, in keeping with the hypothesis that transposable elements are the dominant type of DNA in most eukaryotic genomes, the comparatively large opossum genome is comprised of 52% transposable elements, the most for any amniote sequenced so far.

One of the most intriguing discoveries about the opossum genome is that changes to protein-coding genes seem not to have been the driving force behind mammalian diversification. Instead, non-coding elements with regulatory functions — mostly derived from formerly parasitic transposable elements — appear to underly much of the difference.

Now, I would prefer to just talk about the science here, noting that this is yet another great example of the complex nature of genome evolution, the key role played by “non-standard” genetic processes (Gregory 2005), and the ever-increasing relevance of non-coding DNA in genomics. But, inevitably, I must comment on how this discovery has been reported. Here is what ScienceDaily (which I otherwise like a great deal) said about it:

Opossum Genome Shows ‘Junk’ DNA Source Of Genetic Innovation

(…)

The research, released Wednesday (May 9) also illustrated a mechanism for those regulatory changes. It showed that an important source of genetic innovation comes from bits of DNA, called transposons, that make up roughly half of our genome and that were previously thought to be genetic “junk.”

The research shows that this so-called junk DNA is anything but, and that it instead can help drive evolution by moving between chromosomes, turning genes on and off in new ways.

(…)

It had been initially thought that most of a creature’s DNA was made up of protein-coding genes and that a relatively small part of the DNA was made up of regulatory portions that tell the rest when to turn on and off.

As studies of mammalian genomes advanced, however, it became apparent that that view was incorrect. The regulatory part of the genome was two to three times larger than the portion that actually held the instructions for individual proteins.

I will just reiterate two brief points, as I have already dealt with some of these topics in earlier posts (and will undoubtedly have to do so again in the future). One, very few people have actually argued that all non-coding DNA is 100% functionlesss “junk”, and no one is surprised anymore when a regulatory or other function is observed for some non-coding DNA sequences. Moreover, transposable elements are more commonly labeled as “selfish DNA”, and it has been noted in countless articles that they can and do take on functions at the organism level even if they begin as parasites at the genome level. Two, yet again we are talking about a small portion of the genome such that this should not be considered a demonstration that all non-coding DNA is functional. In particular, the authors identified about 104 million base pairs of DNA that is conserved (i.e., shared and mostly invariant) among mammals, about 29% of which overlapped with protein-coding genes. In other words, about 74 million base pairs of non-coding DNA, much of it derived from former transposable elements, is found to be conserved among mammals and shows signs of being functional in regulation. The genome size of the opossum is probably around 3,500 million bases, which means that this functional non-coding DNA makes up 2% of the genome.

A note to science writers. There is nothing surprising about some sequences of non-coding DNA having an important function. The notion that all non-coding DNA has long been assumed to be completely functionless junk is a straw man. And to avoid misleading readers, you really need to specify that most examples of non-coding DNA with a function represent a very small portion of the total genome.

___________

References

Gregory, T.R. 2005. Macroevolution and the genome. In The Evolution of the Genome (ed. T.R. Gregory), pp. 679-729. Elsevier, San Diego.

Mikkelsen, T.S., M.J. Wakefield, B. Aken, C.T. Amemiya, J.L. Chang, S. Duke, M. Garber, A.J. Gentles, L. Goodstadt, A. Heger, J. Jurka, M. Kamal, E. Mauceli, S.M.J. Searle, T. Sharpe, M.L. Baker, M.A. Batzer, P.V. Benos, K. Belov, M. Clamp, A. Cook, J. Cuff, R. Das, L. Davidow, J.E. Deakin, M.J. Fazzari, J.L. Glass, M. Grabherr, J.M. Greally, W. Gu, T.A. Hore, G.A. Huttley, M. Kleber, R.L. Jirtle, E. Koina, J.T. Lee, S. Mahony, M.A. Marra, R.D. Miller, R.D. Nicholls, M. Oda, A.T. Papenfuss, Z.E. Parra, D.D. Pollock, D.A. Ray, J.E. Schein, T.P. Speed, K. Thompson, J.L. VandeBerg, C.M. Wade, J.A. Walker, P.D. Waters, C. Webber, J.R. Weidman, X. Xie, M.C. Zody, J.A.M. Graves, C.P. Ponting, M. Breen, P.B. Samollow, E.S. Lander, and K. Lindblad-Toh. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167-177.



3 comments to Non-coding DNA and the opossum genome.

  • TheBrummell

    transposons, that make up roughly half of our genome and that were previously thought to be genetic “junk.”

    ACK! Do science journalists only read current-issue articles and ‘classic’ articles more than 50 years old?

    I’m pretty sure McClintock speculated about some function of transposons, in the papers that originally described them. Where does this idea of each and every big new paper overturning vast realms of theory come from?

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  • Chris Harrison

    Where does this idea of each and every big new paper overturning vast realms of theory come from?

    It comes from science writer’s urge to add revelation to their piece. It’s annoying, but journalists almost can’t help but play up non-points (junk-DNA has function) as if they were truly news.

    Thankfully, your advisor at least makes an attempt to mop up sloppy science writing on his blog!

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  • Anonymous

    Barbara McClintock didn’t think of her “jumping DNA” as junk, but she called them “controlling elements.”

    The term “junk” was attributed to so called “repetitive DNA” discovered by Britten and colleagues, who didn’t know at the time (in the sixties), that it had any relationship with “jumping DNA”. The two were combined in the late eighties with the the discovery of repetitive families sharing common ancestors (active jumping DNA, called source/master genes and now transposable elements).

    The term “junk DNA” came mostly from two influential papers by Doolittle & Sapienza, and Oregel & Crick, published in Nature in 1980.

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