Jumping genes and our viral forebears

Your DNA isn't what you think it is - so what is it?

In the beginning, there was the gene. The gene, made of DNA, gave instructions to build (molecular) structures, known as proteins. They sent out their instructions via messengers, called messenger RNA, or mRNA for short. Knowing this, you’d think all, or most of the genome (a word meaning all of the nucleic DNA in a single cell) is made of genes. But you’d be wrong, sometimes dramatically so. In humans, DNA which is used in genes (also called coding DNA) accounts for about 1.2%. 1.2%!!! So what is the rest doing? Is it just junk?

Dawkins and the selfish gene

An important mental leap that was necessary for me was an understanding of the unit of selection first brought to public attention by prominent zoologist Richard Dawkins. The unit of selection, simply, is the smallest unit on which natural selection can act. Instinctively, we say (or, I did) the unit of selection is the organism. Because we can see that. We can see organisms in populations being more or less reproductively successful based on certain traits and this changing what the population looks like in future generations. For instance, if we wanted, we could see male peacocks with less impressive plumage being ignored by female peacocks, leading to more extravagant plumage throughout the population in the future because those with less impressive plumage can’t reproduce. It’s pretty simple, unfortunately, it’s too simple.

The smallest unit of selection, Dawkins argued, is the gene itself. More specifically, it’s stretches of DNA, regardless of whether they code for proteins. What does this mean? In one sense, it means that like animals in the savannah, your genes are in a constant battle for survival with…each other. Scary thought. More reassuring is, by and large, they’ve found the best way to survive is to cooperate, like a zebra herd or a school of fish. So your genes aren’t going to eat each other. That’s a relief.

McClintock and the jumping gene

All your genes coexist because working together they are stronger. Well, mostly. Interesting is that many stretches of DNA, known as transposons, first discovered by Barbara McClintock, are very good at one thing, and, as far as we know, one thing alone: helping themselves. What they like to do is send out a message using mRNA, and create their own protein called transposase. What transposase does is attaches itself to the end of a transposon, and helps it move. Why? Move where? Anywhere it wants, in hopes it wi

ll be more successful. It’s a jumping gene. More interesting still are retrotransposons.

Retrotransposons make lots of mRNAs, some of which make the protein retrotransposase. This is a clever protein which can turn the mRNA into DNA and insert it at any random point in the genome whenever there is a break in DNA (this happens a fair bit, and is fixed up pretty quickly). The effect of this is that retrotransposons copy and paste themselves into various parts of the genome and they start taking over the genome. Of course, if they come in a problematic place, the cell will probably die and won’t be replicated. But if you try something enough times, you’ll be successful eventually (right?) Well retrotransposons work. It’s estimated that over 40% of the entire human genome is made of retrotransposons, including nearly the whole Y chromosome.

Oh yeah, where do retrotransposons come from? It’s pretty simple: viruses. Some viruses, known as retroviruses, have the ability to insert themselves into the host genome. The most prominent example of this is the Human Immunodeficiency Virus, or HIV. So somewhere in history, a virus, or multiple viruses, inserted itself into one of our ancestor’s genomes, and the viral DNA is still floating around inside of us. So in a sense, you’re more than 40% virus. Sorry.

Transposons and evolution

It’s easy to think of transposons and retrotransposons as freeloaders in the genome, doing very little productive and not helping us (if we still think of ourselves as a unified, single living thing, which you probably do – it’s a hard belief to shake). But they sometimes do more than this, albeit by complete accident. I’ve already noted how some transposon and retrotransposon jumps can be deleterious (a fancy word for bad), causing cell death, or even organismal illness. But some, again by complete coincidence, land in the middle of coding DNA (genes), and actually mix with the gene to create a completely new gene. This process is known as exon shuffling: the exons (for our purposes, synonymous with genes), are being shuffled.

This will cause a difference in the life of the organism, whether a big or small one is dependent on where it happens. But surely enough, every now and again, the change is a good evolutionary adaptation, and future populations will have more and more of this entirely new gene. This isn’t too common - in humans researchers estimate around 44 genes came about this way (out of at least 25,000, so somewhere between 0.001 and 0.002%)*.

The end

Understanding how our genome came to be our genome can be overwhelming. If your idea of who you are is rooted in your DNA, it can be quite challenging on a philosophical level. But (too me at least) it’s worth it in realising that this seeming firestorm of molecular movements and chaos resulted in, against all odds and the laws of thermodynamics,** some kind of unified organism capable of reading this and, hopefully, understanding a little more about how it came to be.

I hope you learnt something new!

Read more:

https://www.youtube.com/watch?v=_cJfsWYR42M&feature=emb_logo - a video going far more indepth into how transposons work (it's easy enough to follow, but is 38 minutes long, and is only part 1)

https://science.sciencemag.org/content/371/6531/eabc6405 - new research showing some genes which are believed to have originated via transposons

*The number of genes in the human genome is quite a contentious topic, based on a more contentious topic – what constitutes a gene. But that’s for another time.

**I'm just kidding - our existence doesn't defy the laws of thermodynamics. Nothing does. Nothing.