Increasing piles of genetic junk: LINEs

Posted by ERV on June 4, 2010
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Long interspersed repetitive elements (LINEs) make up a HUGE portion of the junk in your genome.

They dont have any mystical, magical, purposeful functions.

They arent ABSOLUTELY NECESSARY for anything, and technically, they cause trouble when they happen to plop themselves upstream of a gene and are thus negatively selected against, but I digress…

LINEs are kinda relatives of retroviruses that got trapped in our genome. Our genome doesnt really have an efficient way of cutting them out, though our genomes do try to keep LINEs quiet via epigenetics, and usually LINEs are totally non-functional due to mutations. And LINEs dont disappear on their own– cutting themselves out of a genome is not part of their life-cycle. They copy themselves, and plop down in a new spot (copy/paste, not cut/paste). Selfish DNA.

So we have accumulated hundreds of thousands of these guys in our genomes.

I just read a neato paper where they used high throughput sequencing to find/compare human-specific LINEs in 25 people.

High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes.

They conclude that:

  • LINEs are super useful for determining/tracing human ancestry. As Im sure you all have heard me mention before, new bits of junk that arent ‘supposed’ to be there make excellent connect-the-dots pictures for ancestry (this isnt new, but its still neat).
  • Any two people had ~285 differences in human-specific LINEs (148 minimum, 422 maximum). I have some you dont have, you have some I dont have.
  • They did not check to see whether these LINEs were homozygous (in both copies of your genome). There is probably even more diversity here– I have some LINEs you dont have, but some of them are just on one of my two copies of DNA in each cell. Since we only pass on one copy of our DNA to our offspring, this has an effect on how fast/whether new LINEs are fixed in a population or not. Genetic drift, w00t!
  • The older the LINE, the more likely we all have it in common (we are all related!).
  • Brand spanking new LINEs pop up in ~1/140 births. So, of the ~6 billion people alive today, there are ~30 million new LINEs between us all. If all of these junk LINEs are precious and specially created by Teh Designer, all of us without the new sacred LINEs should be dead. We aint. So…

Its just junk, but its still neato!

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Comments

  1. #1 Pierce R. Butler
    June 4, 2010

    So Long Interspersed Nuclear Elements turn out to be rather useful after all, eh?

    How long until the creos use this to claim that the Holy Designer put them into the genome for just this purpose, thus proving that there’s no such thing as junk DNA?

  2. #2 harold
    June 6, 2010

    Despite his benighted attitude toward high quality beer, Larry Moran’s blog is great.

    All the various categories of DNA which come under the rubric “junk” are intense evidence against ID/creationism, because they confirm hierarchies of common descent, and their existence is best explained by mechanisms that are consistent with evolution.

    It is also true that in some experimental settings, removal of large amounts of certain types of “junk” DNA has impacted on the resulting phenotype only in subtle, albeit interesting ways.

    http://www.nature.com/news/2010/100221/full/news.2010.82.html

    In other experimental models, more profound effects of deletion of “junk” regions have been observed.

    http://www.sciencemag.org/cgi/content/abstract/324/5929/935

    These are just a couple of examples.

    ID/creationists have a problem with all of the diverse categories of “junk” DNA.

    They deal with that problem in a characteristic way – first they play on semantics to create a straw man (“scientists claim that ‘junk’ DNA has no function whatsoever under any circumstances”), and then they go from that to a non sequitur (“therefore if any ‘junk’ DNA has any ‘function’, ‘scientists’ are ‘always wrong’ and ID/creationism wins by default”). This pitiful display should not influence scientific study of any type of DNA in any way whatsoever.

  3. #3 Edward Braun
    June 8, 2010

    @harold – I think your last paragraph is spot on. ID/creos are constantly pushing the idea that a study showing some function of non-coding DNA proves that ALL “junk DNA” is functional…therefore God exists! However, I think some (many?) science journalists facilitate the ID/creo argument (hopefully inadvertently). These science journalists do this by incorrectly calling non-coding DNA “junk DNA”. They should call it what it is — non-coding DNA!

    The Nature news feature strikes me as an example of this unfortunate tendency of some science news writers to use “junk DNA” when they should use “non-coding DNA”. We’ve known non-coding DNA has important functions in a wide variety of organisms for a very long time. The Nature feature seems to simply be non-coding DNA that has a function related to the regulation of very distant genes. Very very interesting, but not paradigm shifting. And certainly not a demonstration that “junk DNA” has a function.

    The Science paper is also really cool. Oxytricha is one of the most interesting members of a really interesting group (the ciliates). One interesting thing about Oxytricha is the extensive genome rearrangements they undergo as a natural part of their life cycle. The existence of the rearrangements is surprising but it doesn’t strike me as surprising that transposases were exapted to function for rearrangements. Also very very interesting, but certainly not evidence of functional “junk DNA” like the ID/creos want to believe.

    Plus — even if it was evidence that all putative junk DNA in Oxytrich was functional — it might be viewed as evidence that God is a ciliate. Not sure how the folks at the Discovery Institute would process that.

  4. #4 redacted in case :o
    June 9, 2010

    So today a request comes in to validate some microarray data via qPCR. Part of the gene list is 10 copies of the LINE based reverse transcriptase. *headdesk*

    (not a mammalian system so at least they didn’t pick 10/100,000)