Not So Junky DNA and Beware the Genome SPace INvaders

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Decoding the human genome found that only about 10 percent of the 3 billion or so base pairs of the DNA in the human genome consists of genes that code for proteins. The remaining 90 percent didn't have any obvious function, so researchers called it "junk DNA."

http://www.stern.de/_content/50/44/504448/dna_500.jpg

A new report in Genome Research by researchers at the Genome Institute Singapore find that it's not so "junky" after all:

Using the latest sequencing technologies, GIS researchers showed that many transcription factors, the master proteins that control the expression of other genes, bind specific repeat elements. The researchers showed that from 18 to 33% of the binding sites of five key transcription factors with important roles in cancer and stem cell biology are embedded in distinctive repeat families.

Over evolutionary time, these repeats were dispersed within different species, creating new regulatory sites throughout these genomes. Thus, the set of genes controlled by these transcription factors is likely to significantly differ from species to species and may be a major driver for evolution.

This research also shows that these repeats are anything but "junk DNA," since they provide a great source of evolutionary variability and might hold the key to some of the important physical differences that distinguish humans from all other species.

In other words, these apparently long boring stretches of repeat DNA base pairs are central to determining which genes turn on when and by how much. In addition, some of these DNA repeats jump around inside genomes changing the expression of genes and the course of a species' evolution.

University of California, San Francisco neurologist Raymond White speulates:

"This hypothesis for formation of new species through episodic distributions of families of gene regulatory DNA sequences is a powerful one that will now guide a wealth of experiments to determine the functional relationships of these regulatory DNA sequences to the genes that are near their landing sites. I anticipate that as our knowledge of these events grows, we will begin to understand much more how and why the rat differs so dramatically from the monkey, even though they share essentially the same complement of genes and proteins."

Even more amazingly, biologist Cedric Feschotte and his colleagues at the University of Texas in Arlington have found that some DNA repeats have actually jumped between mammalian and other tetrapod species including African clawed frogs, anole lizards, South American opposums, brown bats, mice and rats. This kind of horizontal interspecies DNA exchange happens among single-celled organisms all the time, but biologists find it very surprising that it can happen between large multicellular species. The repeat sequences have been dubbed "SPace INvaders" or SPIN transposons and may have been carried into these animal genomes by a virus 45 to 15 million years ago.

And this SPace INvasion may have been responsible for a mass mammalian extinction. According to The New Scientist

The team thinks that the hAT transposon invasion occurred about 30 million years ago and spread across at least two continents. "It's like a pandemic, and one that can infect species that weren't genetically or geographically close. It's puzzling, scary almost," Feschotte says.

It may not be a coincidence that the time of the invasion coincides with a period in evolutionary history that saw mass mammal extinctions. This is usually attributed to climate change, Feschotte says, but it is not crazy to suppose that this type of invasion could contribute to species extinction.

The hAT transposon does not occur in humans, but some 45% of our genome is of transposon origin.

Feschotte's work on the hAT transposon is the first time that a "jumping gene" has been shown to have entered mammalian genomes, and the first time it has been shown to do so in at around the same time, in a range of unrelated species, in different parts of the world.

Feschotte admits that we cannot rule out another transposon offensive occurring in mammals….

Whole press release on junk DNA's new usefulness here. New Scientist report on SPIN here

NEXT: Happy Birthday, Bob Barr!

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  1. This rings very true to me. I never liked the idea evolution was propagating vast amounts of useless code for no good reason.

    This strikes me as analogous to the acres of old code the Programmer-Archaeologists would dig through in Vinge’s Deepness novels — instructions that may or may turn out to be useful in a given millennium, but kept around for their potential utility.

  2. Yet more disproof of the false doctrine of evolution. Ramen.

  3. In Bear’s Darwin’s Radio chunks of junk dna would “turn on” causing the next big jump in human evolution.

  4. Dave, did you read Fire in the Deep? What’s up with those tree alien things?

  5. Wait a minute.

    Let’s see if I have this straight, because I just skimmed through it.

    You’re saying that New Scientist had an article that is not about the environment? Did they change their editorial policy recently?

    I do notice that the article does contain the phrase “climate change” though, so maybe not.

  6. zoltan,

    The skroderiders are cool. I have a plant that sits on a little wheeled platform and I refer to it as a skrode.

    Its clearly a lesser skroderider.

  7. LOL, robc. I liked them, but it was a little trippy to think about pine trees attached to skateboards as intelligent life. Good idea, though.

  8. Vinge creates neat aliens.

    The Tines were also great. An individual created via pack mind that could survive changing members (depending on the flexibility of the members). Peregrim being a very loose soul while other souls were more tightly bound to the individuals. Really cool idea.

    The whole science/art of combing members to create packs with specific traits. The “perversity” of keeping a soul alive via incest. The internal war between the souls fighting for control of Tyrathect.
    Did Flenser or the schoolteacher really win? And why didnt he realize it? Is it much like outsiders are more aware of changes in our personalities than we are?

    Just some wonderful concepts.

    Plus nifty hi-tech gadgets.

  9. “Even more amazingly, biologist Cedric Feschotte and his colleagues at the University of Texas in Arlington have found that some DNA repeats have actually jumped between mammalian and other tetrapod species including African clawed frogs, anole lizards, South American opposums, brown bats, mice and rats.”

    Hey, not so amazing. When I’ve been drinking, I look and act just like an anole lizard. It never hurts to get in touch with your scales, now and then.

  10. Thanks a lot – – I just gave away 60 trillion base pairs of DNA code to the salvation army.
    “Hello – Salvation army – yeah, my mon threw out my collection of DNA. Yeah, has a lot of sentimental value. Could I come down to the collection depot and get back.”
    Thanks!!! I’ll be right down.
    Hey, if its mixed in with the good stuff, I’m taking the good stuff.

  11. Alan Vanneman | November 7, 2008, 1:06pm | #

    Hey, not so amazing. When I’ve been drinking, I look and act just like an anole lizard. It never hurts to get in touch with your scales, now and then.

    Note to self, when drinking with Alan do not, I repeat DO NOT, attempt to hang him from your ear lobes.

  12. Yawn. The SPIN element thing is new, but I worked on stuff like this during my Master’s thesis. I even got the paper to prove it, which my thesis advisor expanded on here. For more info, check these out.

  13. High school biology did not prepare me for this.

  14. In Bear’s Darwin’s Radio chunks of junk dna would “turn on” causing the next big jump in human evolution.

    Yup. Beat me to it. But the book kind of gets deep-sixed conceptually if this report is valid.

  15. In Bear’s Darwin’s Radio chunks of junk dna would “turn on” causing the next big jump in human evolution.

    So libertarians are Sci-Fi geeks as well as skewing INT(P/J). No wonder the world hates us 😉

  16. Episiarch,

    But the book kind of gets deep-sixed conceptually if this report is valid.

    Yeah. I didnt think it was one of Bear’s best anyway. The cold war killed Eon, science kills this one, he cant catch a break. I dont think Moving Mars has been invalidated.

  17. End of the cold war killed Eon. Obviously. It depended on the cold war. Also, wasnt the Atlanta-Kiev exchange in 1996?

    I thought is was amusing when Atlanta got the 1996 olympics. 🙂

  18. Hmmm…first Stripes, now Eon. This seems to be “things I like but havent thought about in 15+ years” day.

  19. I’ve never liked the phrase “junk DNA” because how do you prove a negative like “DNA with no purpose”?

    I’m not very surprised by these findings, but it’s nice to have one’s suspicions vindicated.

    TallDave – polymerase slippage

  20. …some DNA repeats have actually jumped between mammalian and other tetrapod species including African clawed frogs, anole lizards, South American opposums, brown bats, mice and rats.

    Possums (South American and otherwise), bats, mice and rats are all mammals. Assume that Bailey actually knows this and that this is some sort of typo. Please clarify.

  21. part of the “junk DNA” problem was that it suggested that the base pairs were “useless” – assuming that they are purposive, causing X. it seems more reasonable to conceptualize it as “as a consequence of their existence, X happens/ed”

  22. or whatever

  23. Tonio: “mammalian and other tetrapod species” — frogs and lizards aren’t mammals, but they are tetrapods. and they too have pretty much the same SPIN repeats as the mammals listed.

  24. Ron Bailey,

    Tonio: “mammalian and other tetrapod species” — frogs and lizards aren’t mammals, but they are tetrapods.

    Well, of course…

    Oops, I think we’ve both misread each other.

    When I read “jumped between mammalian and other tetrapod species,” I assumed that you were claiming that all the critters listed after the word “species” were non-mammals.

    Sorry for the confusion, and damn the ambiguous modifier chains in the English language.

  25. zoltan,

    I don’t know, but I alwasy wanted one!

  26. Ronald Baily

    “A new report in Genome Research by researchers at the Genome Institute Singapore find that it’s not so “junky” after all”

    The “new report” link takes you to the PNAS paper that you mention later, not the paper in Genome Research and the excerpt you provide is certainly not from the article itself.

    I am assuming that the article you are referring to from Genome Research is: “Evolution of the mammalian transcription factor binding repertoire via transposable elements”

    Lastly:

    “In other words, these apparently long boring stretches of repeat DNA base pairs are central to determining which genes turn on when and by how much.”

    The “long” stretches of DNA you are referencing are not long at all as they are transcription factor binding sites and are only 6-10 base pairs long. These are regions where transcription factors (proteins coded elsewhere in the genome) bind to the DNA to initiate translation of other genes (this is why they are called master control genes). These binding sites facilitate evolutionary change because they are so short. One can imagine how a nonsense 6 base pair region of the genome can experience a point mutation which renders it a new transcription factor binding site. The interesting point of the article is that these small transcription factor binding sites have been located in transposable elements that have been incorporated into the genome via horizontal gene transfer.

    You pretty much missed the boat on this one. There is still a lot of junk DNA out there.

    Finally to Warty
    “Yet more disproof of the false doctrine of evolution. Ramen.”

    Please explain this one to me. Maybe after Mr. Bailey cleans up his article it will help you to understand the theory that explains the diversity of life on Earth.

  27. darwinist – I suspect Warty is kidding. “Ramen” is “amen” for adherents of the Flying Spaghetti Monster.

  28. So “If ____ Then Goto” statements outnumber “Print” statements in our DNA. That makes sense.

  29. Plants tend to have reticular phylogenies, but I’m surprised to hear about horizontal DNA transfers in animals. Well, I guess nature is full of surprises.

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