James and the Giant Corn Genetics: Studying the Source Code of Nature

Tranposons are one of those really cool features of genomes that never really seem to make the jump into the public eye. Most people at least have some conception of what a gene is. It’s a piece of DNA that contains the instructions for making a protein plays some role in the cell. A lot of other people can recall hearing an off-hand statistic only some tiny fraction of the human genome is made up of genes, with the rest being “junk DNA”. The question of why most of our genomes have no apparent function is why there’s a slow trickle of scientific research that gets picked up in the popular press as “scientistists discover junk DNA not junk after all!”.

But the reason most of genetics-genomics people aren’t in a huge rush to discover the hidden function behind most of this “junk DNA” is because we KNOW what most of it does and where it comes from. It’s not junk, it’s selfish DNA. <– although there’s certainly lots of cool stuff remaining to be discovered in the much smaller fractions of genomes we can’t classify at all.

The difference between junk DNA, and selfish DNA is quite large. One has no apparent function, the other has as a clearly defined function, just one that doesn’t (usually) benefit the organism whose genome that selfish DNA is hanging out in.

Transposons are anything by random DNA. Some contain whole genes that produce proteins devoted to duplicating the transposon. Others don’t even go to that much effort, but instead simply contain recognition sequences to fool the proteins made by other transposons into helping them move.*

Moving around the genome (and making new copies of themselves in the process) are how transposons manage to survive, and sometimes thrive, in genomes without actually helping their host organisms to better survive and reproduce — the two ways a new gene, or new version of an old gene can spread throughout a population.

To understand how this works, imagine a useless bit of DNA that is found only in a single … platypus. Whenever that platypus reproduces, there is a 50% chance its baby will also carry the useless chunk of DNA. But assuming the total population of platypi/platypuses/platypodes isn’t expanding, the average platypus will only have two offspring that survive long enough to have babies of their own. Since only 50% of them got the useless gene in the first place only one platypus survives to pass the useless DNA to one of its two successful offspring, and so on.** That useless DNA is going nowhere fast.

But now imagine that useless DNA knows how to make lots of copies of itself, which get inserted thoughout the genome of our first platypus. Now almost all of that platypuses offspring will inherit at least once copy of of the useless DNA. And that copy will their their genomes with new copies (include the chromosomes they inherited from their other parent), so all of their offspring will inherit the — functionally useless — bit of DNA. In this scenario, the transposon will, on average, go from being found in only one platypus, to two, to 4, to 8, to 16 and so on. In only ten generations we’d expect it to be found in the genomes of more than 1000 platypodes.***

That, in a nutshell, is what transposons are, and how they came to be some common in the genomes (from corn to our own) without giving anything back**** to their host organism.

*Transposons that make all the proteins they need to move on their own are called autonomous transposons. Transposons that need proteins made by other transposons are called non-autonomous transposons.

**In reality, due to the way genetic drift works, a useless piece of DNA that’s present in only a few individuals will eventually be lost entirely. If there’s a 50% chance a given baby platypus will inherit the useless DNA, there’s a 25% chance they’ll both inherit it, and the number of copies of that particular bit of useless DNA in the population will go up. However, there’s also a chance neither of them will inherit it (also 25%) — there’s also a chance this platypus will have only 0 or 1 offspring survive long enough to reproduce. If the copy number goes up a little, it can always come back down a little, but once it hits 0, it never comes back. Even a small chance of a rare piece of useless DNA being lost from the population adds up to a high likelyhood that it will eventually disappear completely over dozens or hundreds of generations.

***If any DNA that wanted to could duplicate itself as much as it wanted, life as we know it would quickly end, the victim of a terminal case of genome bloat. Most organisms have whole systems that attempt to prevent transposons from duplicating (sometimes more successfully than others). But telling you about those defenses would demand a whole week of its own.

****Anything doing so much to reshape the genome the way transposons do is going to end up occasionally changing things for the better, and I’ll touch on a couple of possible examples of that later this week.