ERVs: Its ALWAYS the guys fault, isnt it?

Posted by ERV on July 5, 2012
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The questions I get asked most often are:

  1. How many ERVs are there?
  2. How many do we have in common with chimpanzees/gorillas/orangutans/etc?

Its hard to answer this.  Depends on what your definition of ‘ERV’ is.  Because sometimes scientists mean a complete/nearly complete ERV (LTR-gag, pol, env-LTR), and sometimes they mean either LTR, Gag, Pol, or Env, or any combination.  There are very few of the former, and a lot of the latter.

But how many are there total?  Well, its hard to say.  Sure, we sequenced the human (and chimpanzee, etc) genome, but we skipped a lot of the parts that are just stretches of repetitive DNA.  Youll often find ERVs here, so youre missing them.

A group of scientists decided to do something fun– Look for ALL the ERVs in 18 different mouse strains:

All the mouse ERVS?

 

The genomic landscape shaped by selection on transposable elements across 18 mouse strains.

And they found some cooooool stuff!

34,773 ERVs (and 28,951 SINEs, 40,074 LINEs)

They didnt find any ‘rabbits in the Precambrian‘– “This primary phylogeny matched the
phylogeny expected from the heritage of the mouse strains”.  In other words, the ERVs were where they were supposed to be if evolution is true.  Thank goodness.  :-|

The half-life for an ERV to become a solo-LTR is about 0.8 million years.

There are fewer ERVs on the X-chromosome– 2/3 what you would expect if everything was random.  “Male insertion bias”. heh. The authors say: “We propose that the vast majority of all TE insertions in the Mus lineage have occurred in the male germline genome.” Which kinda makes sense.  A female is infected with a retrovirus, she has a set number of eggs that could become infected.  A male is infected with a retrovirus, he can produce TONS of sperm infected with a retrovirus, and he has a lot more breeding opportunities.

ERVs are usually in junk DNA.  Why? Cause its not as likely to kill the organism (and thus be selected against).

ERVs are in backwards.  If this didnt matter, they would have expected a 50% to be going forwards, and 50% to be going backwards, but it was only 32.8% going forwards.  Most were going backwards.  Why?  Think about your genes in your DNA like you read a sentence, from left to right.  If your normal transcription machinery is reading left to right, and there is a retrovirus sitting there going left to right, your machinery might accidentally make a retrovirus.  BAD.  But if there is a retrovirus there, plopped in the opposite direction as your genes, your machinery is LESS likely to accidentally make babby retroviruses.  Less likely to kill the organism.

What about the idea that ERV promoters, LTRs, are contributing to cellular gene expression levels?  They really coudnt find any evidence of that, however, there might be something cell-specific that they just couldnt tease out with their methods.

So, ERVs are from the males, theyre backwards, they like junk, and they dont do anything useful.  HA!  HAHA!

BUT, the next time you want to stick it to a Creationist, and you want to use ERV data, use the mouse data.  Its better.

  1. How many ERVs are there?  34,773
  2. How many do we mice have in common with chimpanzees/gorillas/orangutans/etc other kinds of mice?  All of them!
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Comments

  1. #1 Wilfred
    July 5, 2012

    The interesting question would be if they could identify useful coding erv’s, wouldn’t it?

  2. #2 db0
    July 5, 2012

    How is it that you appear to be incapable of typing an apostrophe?

  3. #3 Optimus Primate
    July 5, 2012

    Dang, db0, you’re the first person to ever notice that. I wonder why no one has ever picked up on Abbie’s disdain for apostrophes before.

    I guess we were just waiting for someone of your intellect to come along and point out what we simply couldn’t notice on our own.

    *slow clap*

  4. #4 db0
    July 5, 2012

    Hey, you’re really funny! I’m sure everyone’s picked up on THAT before.

    Point is, one isn’t really worth shit as a writer if one cannot follow one of the most fundamental rules of grammar.

    And don’t try to cast this as “disdain” as though there’s some noble countercultural impetus behind it. I mean, I’m sure you’re a brown-noser, but even that should have limits.

  5. #5 Janicot
    July 5, 2012

    I assume you’re talking about plural acronyms. I’ve always thought that they were messy and unneeded — from an internet copy of a copy of some text from the ‘Taligent Style Guide’:

    The formation of plurals and possessives is usually pretty straightforward, except in the case of abbreviations and acronyms. The following rules should help.

    To form the plural of an abbreviation, a number, or a capital letter used as a noun, simply add an ‘s’ to the end.
    - A group of MPs
    - The late 1940s
    - Mind your Ps and Qs

    To form the plural of an abbreviation with periods, a lowercase letter used as a noun, and abbreviations or capital letters that would be ambiguous or confusing if the ‘s’ alone were added, use an apostrophe and an ‘s’.
    - A group of M.P.’s
    - The x’s in the equation
    - Sending SOS’s”

    I hope the formatting isn’t too bad, but unless I’m confused (not unlikely), the apostrophes seem to be ok in the post.

  6. #6 kad
    July 5, 2012

    db0, you read the artcle, right? Or did you you just scan the sentences for grammatical mistakes? Cuz if that’s what you did, then you missed a pretty cool subject that further supports the truth of evolution from an interesting angle. Get past your pettiness and you’ll see there’s something worth reading there.

  7. #7 Handles
    July 5, 2012

    dbo, go read an original version of Alice in Wonderland, and note how Carroll uses apostrophes: “sha’n't”, “wo’n't”. Think about how language changes and evolves. Feel excited to be part of a time where we might lose even more apostrophes from normal english. After that, slap yourself for stinking up an interesting post with your inane comments.

  8. #8 Skeeve
    July 5, 2012

    I think a lack of apostrophes makes for a great douche detector. It worked.

  9. #9 Ben
    South Africa
    July 5, 2012

    “And don’t try to cast this as “disdain” as though there’s some noble countercultural impetus behind it.”

    I’ll just leave this here:
    http://scienceblogs.com/erv/2008/06/21/death-of-punctuation/

  10. #10 Jerry
    July 5, 2012

    I cant believe my genetics professor never talked about ERVs in class. Never knew they even existed. They pretty much put the icing on the cake on the theory of evolution.

    Lol, people fighting about apostrophe. Gotta love the internet.

  11. #11 Lotharloo
    July 6, 2012

    “How many do we mice have in common with chimpanzees/gorillas/orangutans/etc other kinds of mice? All of them!”

    I’m confused now. Shouldn’t there be some ERVs that insersted themselves into our genome after our lineage split from mice?

  12. #12 Optimus Primate
    July 6, 2012

    Lotharloo, you might be reading on a device that overlooks strike-outs. In the bit you quote above, “chimpanzees/gorillas/orangutans/etc” and “we” are stricken out. So it reads: “How many do mice have in common with other kinds of mice? All of them!”

  13. #13 db0
    July 6, 2012

    Janicot:
    No, I was referring to contractive and possessive apostrophes.
    ITS always the GUYS fault, ISNT it?

    Handles:
    I don’t give a shit what Lewis Carroll did, to be honest! And I don’t feel excited that people like you can reframe failure at writing as “exciting” linguistic evolution, complete with a new example of English being uncapitalised.

  14. #14 Composer99
    July 6, 2012

    Oh noes!!!1! Someone on the Internet hasn’t used apostrophes correctly in a blog post! Whatever shall we do?!

  15. #15 JAB
    July 6, 2012

    I bet db0 has alerted ee cummings editor about their failure to use CAPITOL LETTERS. It’s her style … live with it go away.

  16. #16 Lotharloo
    July 6, 2012

    @Optimus Primate:

    Oh, you’re right. thanks.

  17. #17 Poodle Stomper
    July 6, 2012

    But but but but…ERV!!! Why didn’t they find XMRV in there!?!?!?!? Surely their methods must be super flawed!!!

  18. #18 Handles
    July 7, 2012

    What Lewis Carroll did was considered correct at the time; two apostrophes correctly indicate the omitted letters in “sha’n't”. Far from being a “fundamental rule of grammar”, our modern spelling is a relatively recent convenience born out of laziness. If future rules of grammar omit even more apostrophes, will dbO suddenly become a bad writer? No, his comments suck already, because he has nothing interesting to say.

  19. #19 kereng
    Hamburg, Germany
    July 7, 2012

    How many are “few” complete HERVs? 100? 1000? More?

    I dont understand the “Male insertion bias”, After all, males and females have the same number of offspring. I doubt that infected males will be selected.

  20. #20 daedalus2u
    http://daedalus2u.blogspot.com/
    July 7, 2012

    The issue with reduced number on the X chromosome is more likely (I think) due to males only having a single X chromosome, where females have two. If the single X chromosome gets wrecked by an ERV, that male individual is SOL. A female has two X chromosomes, so the one that isn’t wrecked can rescue the phenotype.

    This is observed in Rett Syndrome, where there is a deletion of MeCP2 which is on the X chromosome. In males it is lethal in utero, in females the presence of active MeCP2 in some cells (due to random X inactivation), rescues the phenotype so they have RS but live.

    If the initial insertion event isn’t too lethal, then in females re-arrangement during meiosis could shuffle the insertion site around, like what happens in the rest of the genome. In males they would just die. That would explain the ~2/3 depletion on the X chromosome.

    When they do similar sequencing on other organisms with different gender determining chromosomes, that is what I think they will find, a depletion of ERVs in the chromosome that is the homozygous gender determining chromosome.

  21. #21 Kemist
    July 7, 2012

    I dont understand the “Male insertion bias”, After all, males and females have the same number of offspring. I doubt that infected males will be selected.

    A mammal female is born with all her ova. The window for insertion and reproduction of a new virus is very small.

    However, males produce new spermatozoids, which can be infected, for life.

  22. #22 Bob Powers
    Tulsa, OK
    July 12, 2012

    ERVs are the trump card proving creationism false.

    It is always interesting to read of yet a new direction this amazing field of science has discovered.

    I’m always astonished how selectively-ignorant (and willfully so) that creationists can be, after being exposed to such science.

    I suppose I shouldn’t underestimate the power of self-imposed ignorance.

    Or of fools, for that matter.