The human genome is about 3.1 billion nucleotides long.

8-10% of your genome is retroviral-ish. We will be conservative and go with 8%– thats 248,000,000 nucleotides of retrovirus.

The average retrovirus is about 10,000 nucleotides long. So we should have ~ 24,800 retroviral elements in our genome.

But there must be more than that, because there usually are not full-length retroviruses left in your genome (they would make retroviruses and kill you). Some have deleted genes, or deleted chunks of genes, or sometimes the entire genome is deleted except for a solo-LTR.

So, some number of retroviruses, greater than 24,800, have accidentally infected our germ-line over the course of human history? I know, I know, I always say “when you are dealing with a time-frame of billions of years, accidents happen all the time”, but so many accidents? It is also implied that accidental retroviral infection happened even more often than what we see now, because we dont see all the insertions that killed the offspring… it just boggles the mind.

A group at Oxford have found one way there can be so many retroviral elements in your (and other mammals) genomes, without requiring each and every insertion to be the result of an independent infectious event:

Env-less endogenous retroviruses are genomic superspreaders

Though Ive said this before on ERV, I will say it again now: Your genome ‘wants’ ERVs to be silent. It ‘wants’ them to be junk. You have evolved numerous defenses against ERVs to keep them from expressing proteins. Since your genome cant forcibly and purposefully cut out an ERV after it has invaded, it does try to keep the genes silent via epigenetics. Then, nature takes its course, and the ERV accumulates mutations that render the genes defective or deleted, and the genome has done the best it can do to protect itself from a selfish gene.

What this group found, is that some ERVs lost their Envelope protein, in a seemingly preferential manner. Like, it didnt just degrade by random mutations. The ERVs lost Env first. When they did that, the ERVs essentially became prisoners. Without Env, there is no way they could ever leave their host cell again.

But its like the ERVs were making the best of their captivity. Sure, they lost Env, but they still had every other retroviral gene at their disposal. This means they could not escape their host cell, but they could reinfect it from the inside as much as they bloody wanted. Just to have fun personifying viruses, its like they were saying “Fine. You wanna trap me here? Imagonnna MESS YOU UP! Ur pretty genome aint gonna be pretty no more!”

Or alternatively, they got Stockholm Syndrome “You want to trap me here?… Okay… I LOVE IT HERE! This place is AWESOME! I am TOTALLY moving in OMFG I LOVE THIS GENOME!! I want to be a part of it forever and ever and ever and EVER! I WILL NEVER LEAVE YOU!!!!”

The end result? 22% of the viral families make up 80% of the retroviral elements in your genome. Which makes more sense than each and every retroviral element in your genome coming from a completely independent infectious event, or a reinfection event.

And really, I cant honestly blame the ERVs for not wanting to leave after they have infected us. Who wouldnt want to be trapped forever in a beautiful, intelligently designed, specially created genome like ours? (and 38 other species of mammal studied in this paper.)

Comments

  1. #1 MarkH
    April 24, 2012

    You know Abbie, it took me a while to get just how powerful this ERV stuff is as a proof of evolution. When I was watching you debate that creationist most recently he kept on bringing up fossils, how there were no transitional fossils etc., and you kept bringing up ERVs. I kept wondering, why not bring up archaeopteryx or tiktaalik? It was two weeks later that I finally understood why you kept responding with evidence about ERVs (other than that it is your field of study). They’re an incredible molecular fossil record. You have the fossils alive and in our genomes right now showing the whole progression.

    I now feel stupid for not getting it, although I also understand why your creationist opponent wasn’t getting it either. I realize this is obvious now, but I don’t think about this stuff as often as I used to.

  2. #2 ERV
    April 24, 2012

    … why not bring up archaeopteryx or tiktaalik…

    Well, yes, it was partially because ERVs are powerful evidence for evolution (if we had never dug up one fossilized bone, ever, evolution would have hit us over the head like a sack of doorknobs once we could sequence genomes).

    But it was also because I cannot pronounce either one of those words. LOL!

    At ‘Skeptics of Oz’ this weekend I needed a prof in the audience to help me with ‘Guillain-Barre’. I swear Im just a geekier version of Zoolander

  3. #3 Poodle Stomper
    April 24, 2012

    This sounds an awful lot like the intracisternal A particles (IAPs) that hop all around the genome of my mice. They may not be able to leave the cell to infect others but they have amazing copy numbers in the cell.

  4. #4 Justicar
    April 24, 2012

    Like any of my ex boyfriends will tell you, once you get in me, I’m always a gracious host. It’s good to know my genome gets along with its captives too; I can sleep easier knowing that.

    AHAHAHAHA From the last link in your article:

    Meyer is a Christian, but atheists, and theists who believe God never intervenes in the natural world, will be instructed by his careful presentation of this fiendishly difficult problem.”

    Reminds me of a Star Trek: Voyager episode where Janeway is Chaotica, and Paris tells her to throw in fiendish and other terms because ‘they love that’.

  5. #5 Camden
    April 24, 2012

    I’m wondering what the process is in the nucleus that deletes the env protein and disables the virus? Could this technique be copied by a drug that could disable HIV or other retroviruses? Did the deletion simply happen by chance over time or is there a specific enzyme that could scissor it out as a gene therapy?

  6. #6 Scott Hatfield, OM
    April 25, 2012

    Droll. But…also…..not entirely unreasonable beyond the metaphor. After all, if I were to believe **SOME** people, viruses are as “alive” as bacteria, and so if I grant that, then a sort of ‘stopgap endosymbiosis’ might’ve evolved in some lineages before the viral program loses all function. Who knows? Perhaps some of the elaborate DNA repair mechanisms in mammals have been ‘fine-tuned’ by the requirement of parsing retroviral artifacts…?

  7. #7 dustbubble
    April 25, 2012

    so .. after the the ERV has had its wicked way with us, our genome strikes back by hiding its pants and shoes??
    Muahahaha, get out of that, badboy!

  8. #8 mo (one of Abbies's elk)
    April 25, 2012

    Poodle Stomper, IAPs are ERVS.

    Abbie, btw,
    Are primates or the human lineage “better” than other animals at perventing retrovirus infection? I’m reading trough Weinberg’s cancer textbook at the moment and it says the youngest ERVs became established in the human genome more than 5 million years ago, while rodents and chicks have younger ones that become mobilized more easily. Also, HIV needs all those accessory genes to be infective.

    Of course, the book is from 2006…

  9. #9 Poodle Stomper
    April 25, 2012

    Abbie,

    Yes, I know that they are ERVs =P I simply meant that they also take advantage of their loss of ability to be secreted while still being able to replicate to spread quite bit throughout the mouse genome. I mentioned this b/c it seems like it could be the same approach. Also because I work on mice and wanted to feel relevant to this thread =D

  10. #10 Poodle Stomper
    April 25, 2012

    Haha, and now that I actually started reading the paper, I see that they mentioned IAPs specifically. Sigh. Next time I’ll read first and then try to contribute after. =(

  11. #11 Roman
    May 2, 2012

    I don´t quite understand these numbers. You say: “8-10% of your genome is retroviral-ish.”
    But BBC Article about this study states: “only 1.5% of the genetic material in our cells codes for human life. Half of the rest is sometimes described as “junk DNA” with no known function, and the other half consist of genes introduced by viruses and other parasites.”
    http://m.bbc.co.uk/news/science-environment-17809503
    If i calculate correctly, half of the rest is about 49%. So what is right, how many percents of DNA is retroviral DNA?

The site is undergoing maintenance presently. Commenting has been disabled. Please check back later!