Evolution 101

Saturday, April 08, 2006

Molecular Evidence 3: Transposons

All right, this is the third podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ll be using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can follow along with me there if you like.

The third piece of evidence is from transposons.

Now, you’ll remember that back in episode 106, we looked at junk DNA, and what it meant. Well, for the past two weeks we’ve been looking at the coding part of the genome, essentially the genes themselves and the products of their transcription, that is, proteins. For the next three weeks we’re going to leave those evidences behind in the coding part of the genome, and we’re going to look at the noncoding part, which some people call “junk.” That’s right- one man’s junk is another man’s treasure, and so-called junk DNA is a treasure of evidence, very powerful evidence in support of evolutionary theory.

Well, what is a transposon? A transposon is a mobile section of DNA. What I mean by saying that it’s “mobile” is that it can literally change its position within the genome. I’m afraid that there really aren’t any good analogies for this, so I’ll just have to resort to some bad ones. You remember that before I said that the genome is kinda like a magazine, where the genes are articles which are separated by pages and pages of advertisements. Well, you know those annoying advertisements that, instead of being printed in the pagestock, are printed on little cards and just kinda stuck in the magazine, near the spine? Or maybe one side of the card is glued to the page with that flimsy, rubbery glue that you have to peel and pull off at the same time? That’s basically what a transposon is. In the same way that those little cards are mobile advertisements, a transposon is mobile DNA.

Let’s say that you’ve got one of those annoying sticky cards in your magazine, and you pull it out. But then you accidentally drop both the card and the magazine, and they both land together. The card is going to be restuck in the magazine, but probably not in the same place. It might be stuck to the front cover. It might be stuck on another advertisement page that had nothing to do with where it came from. Or, it might be stuck on the story that you were reading, obstructing a couple paragraphs and preventing you from finishing the article. Well, that’s also what happens with transposons. A transposon can be cut out of the genome and then reinserted someplace else. The genome is a pretty big sequence, so there’s lots of places a transposon can reinsert. Sometimes a transposon will reinsert at another noncoding region. Actually, this is usually what happens, since there’s so much more noncoding DNA than there is coding DNA. But sometimes a transposon can reinsert in a coding region, and disrupt a gene. Now, in the same way that the stuck card in your magazine prevents you from reading the story, the inserted transposon prevents the gene from being transcribed, effectively turning it off. You might also think of a transposon like a pop-up ad on a website that pops up out of nowhere and obscures the content that you’re trying to see on the page.

Now, one of the obvious questions at this point is: why in the world do transposons exist? They seem pretty annoying, from a strictly genetic perspective, and they also seem dangerous, since by inserting into a gene a transposon could cause a debilitating mutation or disease. And indeed, this is the case- transposons are mutagenic, and are associated with a number of diseases, including hemophilia, severe immunodeficiency, and cancer. So why do transposons exist in genomes at all? Well, you can think of a transposon as existing as a separate selective entity to its host genome- almost like a DNA parasite. Now, admittedly, this is a hard concept to grasp, since we’re talking about a chunk of DNA and not something typically associated the word “parasite,” like a mosquito or a tick. But remember that even though it’s easier for us to think of concepts in black and white terms, science isn’t quite so discrete. Transposons come in two basic types: class I transposons, which are also called “retrotransposons,” and class II, which are simply DNA transposons. Retrotransposons function by allowing their sequence to be transcribed into RNA. It’s at this point that a retrotransposon does something odd- it reverse-transcribes the RNA sequence back into DNA, and this DNA copy of the original retrotransposon sequence is then integrated back into the original genome, but at a different location. Both of these functions are carried out by enzymes whose genes are encoded for within the retrotransposon sequence itself- pretty clever. In fact, this is the same way that retroviruses like HIV work- except that a retrotransposon never leaves the cell in a virus particle. You can almost think of a retrotransposon as a virus that made itself comfortable within an organism and decided never to leave. DNA transposons use a different enzyme called transposase, which actually cuts out the genomic transposon sequence and puts it back into the genome in a different location. This skips the whole process of reverse transcription of RNA that retrotransposons use, but you get the same basic effect.

Retrotransposons themselves come in two basic types- long and short. The longer ones are called “long interspersed elements,” or “LINEs.” The shorter ones are called “short interspersed elements,” or “SINEs.” LINEs contain the two enzymes necessary for the reverse transcription and integration that I already mentioned- called, predictably, “reverse transcriptase” and “integrase.” SINEs, on the other hand, don’t carry these genes, and so are dependent on LINEs for their propagation. You can think of the enzymes used by the retrotransposons as a “copy and paste” function, just like in a word processor. The transposase used by the DNA transposons is more like the “cut and paste” function, however. And I’m sure you know that if you cut and paste words in a document, you may screw up the meaning of the text, but you’re not going to significantly add or subtract to the length of the text. If you copy and paste, though, you’ll find that not only have you screwed up the meaning of the text, but you’ve also added overall length to it, and depending on how many times you paste, you may have added a lot of length to it. And that’s what we see with retrotransposons- both LINEs and SINEs are found all throughout the human genome, for example, and are responsible for nearly 30% of the total size of the genome. 30%! That’s a lot of space wasted on DNA parasites.

But it’s not all for naught. Because so much of the genome is made up of these predictable sequences, and because these sequences occur randomly in different places in the genome, transposons offer an excellent way to identify individuals genetically. I’m sure you’ve heard of technology like “DNA fingerprinting,” or something similar, that is used to establish paternity using a genetic test. These tests take advantage of the fact that two different individuals in a population having the transposon sequences in the exact same location is extremely rare, so much so that you can conclude genetic relation based on similar patterns of genomic transposons. Well, I’m sure you’re all astute enough to realize that if transposons can be used to establish a hereditary relationship between a father and his offspring, it can also be used to establish a hereditary relationship between two organisms from different species! Remember, the only observed mechanism for two organisms to have similar genomic sequence is through heredity, and so if two different species can be shown to have similar genomic sequences, then we can conclude that they share a common ancestry. So we hypothesize that if evolutionary theory is correct, and different species share common ancestry, then closely related species will share common transposon insertions. So let’s look at the evidence.

We’ll look at one of the common SINE retrotransposons, called the Alu element. This is a sequence only about 300 nucleotides long, and it found in all mammal species, and particularly in humans, where it composes close to 10% of the entire genome. In alpha-globin gene cluster, 7 separate Alu elements are known to exist, and all seven are found in the exact same location in the corresponding chimpanzee gene. According to our hypothesis, corresponding transposon sequences imply shared ancestry, and thus this evidence supports evolutionary theory.

So, to review, transposons are mobile DNA sequences that create distinct insertion patterns that allow us to distinguish hereditary links between individuals of the same species, as well as to establish common ancestry between organisms of different species. Once again, the evidence of common transposon insertions in humans and chimpanzees strongly supports the evolutionary hypothesis. Next week, we’ll look at pseudogenes, and how these broken genes also support evolutionary theory. Take care!

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