This spring I sat in on a course in Viral Evolution. I quickly fell madly in love with Patrick Forterre hypothesis: that everything on Earth now evolved from and because of—viruses.
Of course, one of the booby-traps that scientists need to watch out for is… falling madly in love with a hypothesis. You have to look at the data objectively—regardless of how much you might like or dislike an idea.
So even though I cant get into a time machine, go back a few billion years, and watch what happened myself, we can look at our (and other organisms’ genomes) to see if we can find any clues. And that’s the topic of this first paper: Mobile Elements: Drivers of Genome Evolution.
Approximately half of the mammalian genome is composed of mobile elements, cousins of retroviruses. Mobile elements can be in the form of:
DNA transposons: Cut and paste themselves into DNA, normally staying close to the original insertion (‘Local Hopping’), but can move to a distant site in the genome
LTR retrotransposons: Duplicate themselves, rather than cut/paste. They do this by being transcribed into RNA, reverse transcribed into DNA, then inserted into DNA. They are very similar to retroviruses (have gag and pol) but lack a functional env. Endogenous retroviruses fall into this category.
Non-LTR retrotransposons: LINE-1s, or L1s. Only encode a nucleic acid binding protein, endonuclease, and RT. They are reverse transcribed right on the genomic DNA, not in a viral-like particle in the cytoplasm like LTR retrotransposons.
Oddballs: Look like bits from the other groups, but lack all of the genes necessary to be autonomous. They might be missing a protease/integrase/RT/etc.
Okay, well, that’s neat—but what do these bits of DNA have to do with the evolution of genomes? Well, these little guys can really screw around with your chromosomes. Humans have about 80-100 L1s, and about 1 in 50 people have a novel L1. These L1s can plop themselves in the middle of a gene. They can repair breaks in your DNA. Increase/Decrease the transcription of genes. And they (potentially) control X-chromosome inactivation in women! Trust me, that’s a good thing.
L1s also act in trans to activate Alu sequences, or SINES. Alus are only ~300 base pairs long, but they make up 11% of our genome! 1 in 30 people has a *new* Alu. Alus really have the ability to screw around with genomes—they can cause unequal crossovers (instead of two identical chromosomes splitting into two eggs/sperm, one is chromosome is larger, one is smaller), rearrange coding regions, and duplicating portions of chromosomes. And, L1s can do some rearranging of their own, as well.
So what are the effects of these chromosomal rearrangements? Obviously, screwing around with genes can lead to diseases. Alu insertions are the cause of over 20 diseases, and L1s cause some as well. Obviously, there can also be problems with chromosomal deletions, and L1s changing the transcription levels of genes can also have negative consequences.
But, changing transcription levels can also have evolutionarily beneficial consequences. After comparing our genome to the recently finished chimpanzee genome, we noticed that it wasn’t so much our genes that make us different from our chimpanzee cousins, but the transcription levels of the genes we share. Chromosomal duplications can also have a benefit—if you have two copies of a gene, then one of those genes is no longer under any evolutionary pressure. Its free to mutate, potentially creating a new useful gene, or mutate into a pseudogene.
So maybe I cant completely agree with Forterre yet, but obviously, viral elements have played a huge role in the evolution of our genome, and every other organism on this planet.