Monday, June 18, 2007

More Marsupial Madness!!

When I wrote about the new marsupial TCR gene family yesterday, part of which was created by retrotransposition, the last thing on my mind was the latest junk DNA-->crappy journalism scandal*. It was also the last thing on my mind when I did my usual Monday morning PubMed search for 'endogenous retroviruses,' to see what other labs are finding/looking at. And I got well into this paper before I realized, "Oh yeah! This is some of the 'junk' theyre talking about, isnt it?"

Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica.

This paper basically reiterate what Creationists dont want to hear-- We split away from marsupials 170-190 million years ago. Marsupials are an evolutionary branch that connects us to another fully sequenced species (chickens) so we can learn a lot about our evolution by comparing everyone. Transposable elements are great for screwing around with chromosomes (fusions, deletions, rearrangements, etc). And sometimes we co-opt transposable elements for our own use, either as coding genes or non-coding genes (ZOMG SOME JUNK HAS A FUNCTION JUNK HAS A FUNCTION OMGZ!!11!1! GAWD IS REAL!)

The funny part about that last reiteration is that they give a reference that I havent read before:

But an increasingly recognized phenomenon is the co-opting of nonautonomous elements as functional noncoding elements (Bejerano et al. 2006; Kamal et al. 2006). This fulfills the vision originally espoused by McClintock, Davidson, and Britten, that TEs, and repetitive DNA in general, may be critical "control elements" in modern genomes (McClintock 1961; Davidson and Britten 1979).


And ID Creationists are 'geniuses' because they discover this fact 30-40 years after everyone else. Fantastic. Congratulations guys. Hey, nobody tell them about siRNA quite yet-- their heads will explode *rolleyes*

So tranposable elements in marsupials (specifically the short-tailed opossum (pronounced 'possum')) is friggen awesome! 52.2% of their genome appears to be transposable elements, as opposed to 44.8% in humans, and 38.6% of the mouse genome. We've got about the same number of ERVs, transposons, and SINES as possums, but they have a TON more LINEs (29.2% vs our 20.4%). Remember LINEs duplicate by copying themselves (instead of hopping around, like transposons) so they make genomes larger, and theyre GREAT at changing the transcription rates of nearby genes (up and downstream) because of their internal promoters, and their ability to screw around with 'normal' promoters.

These researchers also made a cool 'speculation' as to why ERVs appear to be concentrated in certain regions of this possums genome:
It is tempting to speculate that the regions of high ERV density in Monodelphis indicate the location of ancient centromeres and neocentromeres, or that they could play a role in centromere repositioning.


**If science journalists keep calling ERVs 'junk' Im changing the name of this blog to 'The Junk Yard', I will insist upon being referred to as 'The Garbage Lady', and Arnie will be renamed 'Bad Bad Leroy Brown, the Junk-Yard Puppy'. Thanks to the journalists who realize the damage theyre doing and are trying to learn, and shame on the lazy brats who are too proud to admit they royally screwed up.

1 comment:

The Factician said...

Remember LINEs duplicate by copying themselves (instead of hopping around, like transposons)

A DNA transposon hopping can result in a duplication if the break created by the transposon is repaired by homologous recombination off of a sister chromosome.

In organisms where homologous recombination works better (like bacteria and yeast) most cut & paste DNA transposition events result in a duplication of the transposon due to this type of repair.