8% of Your DNA Comes From a Virus

An anonymous reader writes "About 8 percent of human genetic material comes from a virus and not from our ancestors, according to an article by University of Texas at Arlington biology professor Cédric Feschotte, published in the Jan. 7, 2010 issue of Nature magazine."

Re:Ob. Matrix quote

[dsavi]

Human beings are a disease, a cancer of this planet. You're a plague and we are the cure. Okay that's done with.

Summary and article misleading

[Anonymous Coward]

These are endogenous virus fragments. Which means that a virus inserted itself into your ancestor's DNA. So you didn't get this new DNA after you were born, you inherited the 8% viral DNA from your ancestors.

What a crappy press release

[RNLockwood]

So 8% of my DNA comes from a virus and not from my ancestors? I guess that means that I was infected with the DNA after conception and for some reason it's not heritable since I didn't get any from my ancestors. The big story, then, is that there is a mechanism that excludes the viral DNA during meiosis.

Dr Feschotte must have cringed when he read the release.

the OA refed in the OP link is in N&V section

[mapkinase]

http://www.nature.com/nature/journal/v463/n7277/full/463039a.html [nature.com]

That section is mostly commissioned and if not submissions reviewed by editor (technically, not peer reviewed).

The author of the referred N&V article is the author one of the articles in the reference section...

For peer-reviewed article, I would go for:

http://www.nature.com/nature/journal/v463/n7277/full/nature08695.html [nature.com]

written by bunch of Japanese:

Endogenous non-retroviral RNA virus elements in mammalian genomes

Retroviruses are the only group of viruses known to have left a fossil record, in the form of endogenous proviruses, and approximately 8% of the human genome is made up of these elements1, 2. Although many other viruses, including non-retroviral RNA viruses, are known to generate DNA forms of their own genomes during replication3, 4, 5, none has been found as DNA in the germline of animals. Bornaviruses, a genus of non-segmented, negative-sense RNA virus, are unique among RNA viruses in that they establish persistent infection in the cell nucleus6, 7, 8. Here we show that elements homologous to the nucleoprotein (N) gene of bornavirus exist in the genomes of several mammalian species, including humans, non-human primates, rodents and elephants. These sequences have been designated endogenous Borna-like N (EBLN) elements. Some of the primate EBLNs contain an intact open reading frame (ORF) and are expressed as mRNA. Phylogenetic analyses showed that EBLNs seem to have been generated by different insertional events in each specific animal family. Furthermore, the EBLN of a ground squirrel was formed by a recent integration event, whereas those in primates must have been formed more than 40 million years ago. We also show that the N mRNA of a current mammalian bornavirus, Borna disease virus (BDV), can form EBLN-like elements in the genomes of persistently infected cultured cells. Our results provide the first evidence for endogenization of non-retroviral virus-derived elements in mammalian genomes and give novel insights not only into generation of endogenous elements, but also into a role of bornavirus as a source of genetic novelty in its host.

Re:Bible Code?

[cmiller173]

Actually Down Syndrome (technically Trisomy 21) is having a whole extra copy of chromosome 21 not the lack of one.

Re:Not Bad

[maxume]

Sickle cell anemia originated as a mutation. The mutation happens to confer some defense against malaria, so it became widespread in certain geographic areas and is still present in the population.

That's a small difference in phrasing, but it is much clearer.

Re:Bible Code?

[mapkinase]

"Any sufficiently large set of information is going to give you some matches on just about anything you search for."

That's why the bioinformatics tool the Japanese (authors of the original paper in Nature) were using (called BLAST) has a parameter called an e-value for each sequence similarity hit. It's basically a probability to encounter such hit randomly in a database of that size (assuming the sequences in the database are pseudo-randomly distributed).

That evalue for the found matches is less than 1e-70.

HERVs are ancestral

[angry jimmy]

The posted summary is somewhat misleading. Human endogenous retroviruses (HERVs) are responsible for ~8% of the human genome sequence, but these things haven't been active for a long time in terms of human history - so the 8% that's in your genome now did come from your parents, and their parents etc. until you get back to the time many thousands of years ago when HERVs were actively creating new insertions. The linked summary is a summary of a new finding in which the 'endogenization' of a new class of virus known as a Bornavirus is reported (which exists in only a few copies in humans)

Re:Bible Code?

[reverseengineer]

Just a minor quibble- Down syndrome is caused by having an extra copy of chromosome 21 (trisomy), not a missing copy (monosomy). In humans, monosomy is fatal for the non-sex determining chromosomes (Turner syndrome is the result of monosomy X), and the only somatic trisomy conditions that are remotely survivable much past birth are those of 13, 19, and 21, and each of those has a set of profound symptoms such that they have an associated syndrome (Patau, Edwards, Down). This does nicely illustrate that issues with genetic insertion, deletion, and translocation are not so much a question of quantity as with placement. Trisomy of chromosome 21 is survivable because there aren't enough vital genes affected to cause inviability (the somatic chromosomes are numbered by size, with 1 the largest).

Your genome can tolerate a significant insertion of genes, as long as they don't cause serious trouble. In terms of viral DNA additions, the most significant risk is for a stretch of viral DNA to insert within an existing gene, breaking it and possibly creating a new gene variant that causes harm. This is believed to be a mechanism of viral infections associated with cancers (e.g. Epstein-Barr and Hodgkin's lymphoma, HPV and cervical cancer).

Misleading title

[BurningRome]

The "8% of your genome" comes from the first paragraph of the News and Views article which reviews the actual article by Horie et al, and is referring to ALL viral remnants in the human genome, not just this new Bornavirus one. From a quick scan of the paper, it looks like they didn't estimate what fraction of the human genome comes from their Bornavirus, but they only describe 4 actual elements - so that's a vanishingly small part of the human genome. The vast majority of viral elements in the genome come from retroviruses and other retrotransposons, and that's been known for a long time.

Research was conducted by Keizo Tomonaga in Japan

[jestill]

From the article the research was "led by Professor Keizo Tomonaga at Osaka University in Japan". The article that Cedric wrote was just an opinion piece discussing the research by Dr. Tomonaga.

Re:Not Bad

[digitalunity]

Unless it occurred recently and you're an intermediary state between mutation occurring and the mutation dying out.

Our modern civilization though protects the well being of even those with negative traits who would have otherwise naturally died out. That's not to say evolution in humans has stopped. Instead, we're simply not weeding out the negative traits.

Re:Ob. Matrix quote

[D Ninja]

Ahhh religion, where changing flesh into bread and blood into wine isnt considered "witchcraft". Yet all other "magics" was at one time punishable. Hypocrisy, it loves religion.

While there are some individuals who do believe that the bread and wine become flesh and blood upon consumption, that is a very uncommon view. Instead, the act of communion is period of remembrance of what Jesus Christ sacrificed to cover our sins. His body was tortured as payment for those sins, and his blood was shed to cover those sins. A bit confusing, I understand, especially if you have had no experience with it. But, communion is not what you are making it out to be.

Re:Useful?

[IICV]

In fact, back when lasers were first invented, people referred to them as "a solution looking for a problem". They were so cool, but for a while nobody could think of anything useful to do with them.

Re:Ob. Matrix quote

[Kiaser Zohsay]

Is Teller God? Should I worship him?

Why don't you ask him yourself?

Because he wouldn't answer you.

Re:Ob. Matrix quote

[flitty]

Wat? Transubstantiation [wikipedia.org] is official church Doctrine for over 1/6th of the earth's population, and has been since The Council of Trent in 1551. I know it's simplistic to say that 1 billion people in the church all believe this teaching exactly, but come on, we're not talking about some strange, obscure cult here...

Re:Ob. Matrix quote

[flitty]

Furthermore, I understand that some christian branches, such as Mormons believe what you say, where the water/bread is symbolic, but as far as offical Roman Catholic Church doctrine, Transubstantiation does occur, and is not symbolic. Unless everything i've been taught about the catholics has been wrong, from all sources except for some guy on Slashdot.

Re:Useful?

[Bengie]

I remember reading an article about sheep and virii. Some type of sheep use to have a virus that use to be bad for it. Even though this virus was bad, it did have one good attribute. It reduced the chance of a miscarriage and did it better than another "native" gene.

It so happened that this viral infection reduced the chances of miscarriages enough that at some point the virus stopped being bad for the sheep and they had a better chance to reproduce.

Now days, if you neutralize the virus, the sheep will always miscarry since the old gene got silenced/removed in favor for the virus.

The sheep and virus evolved to live together.

I read this a LONG time ago, i think it was in Discovery mag or something, but I can't remember much more than the idea of the story. The details might be slightly off, but the summary is the same. And they did talk as if the virus was still actually living in the host, not just select genes.

Re:Ob. Matrix quote

[Knara]

Yeah, but Hugo Weaving said it with such style. Hicks had some funny stuff, but really, he was like a more insightful Sam Kinison who didn't yell as much.

Re:Not Bad

[FiloEleven]

If my ancestor got a brain virus, and it is still with us, then it most probably is that that virus provided something very positive compared to the negatives that you speak of.

No. All it means is that whatever changes the virus makes, it doesn't greatly affect the ability (means and opportunity) of those who have it to reproduce. Remember, natural selection, the mechanism through which evolution operates, is not working toward a glorious future of perfection, it is a consequence of how adapted an organism is to its environment. If the organism can reproduce just as much with the virus as without, then it's going to stick around even if all it does is sometimes cause schizophrenia and provides no positive traits.

Re:Useful?

[UnknowingFool]

Well the term "dormant" doesn't mean what it used to mean since the human genome has been mapped. Before the mapping, it was thought that genes or "active" part of our DNA controlled every aspect of processes and the expectation was that humans would have at least 100,000 genes. There is "dormant" DNA in all organisms and it would represent a small part of our genome. That turned out not to be the case. Humans have about 23,000 genes which is fewer than found in corn and many of our genes are common with other plants and animals. The difference it turns out is that while we have the same genes as other organisms, there are different parts of the "dormant" DNA. This dormant DNA while it does not contain any genes contains triggers and modifiers to genes. For example animals all have the same gene to make limbs but the triggers are different in a whale as opposed to a bird as opposed to a human.

Re:Who owns the copyright?

[smellsofbikes]

I'm not quite sure what you're asking. If what you're asking is "how can you tell the difference between originally human DNA and originally virus DNA" my first answer would be that neither one is original. However, past that, one thing that stands out is that viruses have tremendous selection pressure to economize (because the faster you replicate the faster you spread, and the speed of replication is linearly proportional to the length of the genome.) As a result, evolution removes anything that isn't unneeded, and in fact some viruses stack genes on top of one another. To explain that I have to do a bit of cell bio: every three DNA bases code for one protein, so you read DNA by threes. Since this provides for 64 combinations and there are only 20-ish proteins, there is what's called genetic degeneracy: multiple codons map to each protein. As a result, there are lots of viruses that encode one protein by threes, and taking advantage of degeneracy, code for *another* protein by shifting one over and again reading by threes. Given the sequence abc def ghi jkl, one protein is produced that reads off abc:A, def:B,..., while another protein is produced that reads off bcd:G, efg:H,..., and so forth. In some cases, viral DNA can even be read backwards to produce yet another protein.

So if you're looking at a chunk of DNA and it appears to be continuous, particularly continuous and overlapping, it's very likely recently viral, while if it has big chunks of other stuff in it, long promotion/repression sequences, lots of regulatory stuff, it's probably not recently viral. Does that answer what you're wondering?

Re:Useful?

[linguizic]

You must mean gave rise to placental mammals. Not all mammals have placentas (see marsupials and monotremes [which are way cool btw]).

Re:Ob. Matrix quote

[PRMan]

On top of all that, the fact that "The Flood" actually has even earlier recorded sources (Sumerian, for example) just make the whole thing even more, well not maybe comical, but at least mildly amusing.

Yes, amazingly almost every culture on earth has a global flood story with a single boat, a bunch of animals and a negotiation of sorts with a god or gods. There are over 200 of them, involving nearly every culture that was on earth in early history.

For instance, this one from China, where the person is even named Ndrao-Ya.

http://www.archives.ecs.soton.ac.uk/miao/songs/TranslatedSongs/m131/m131tr.pdf [soton.ac.uk]

Here's a handy chart to summarize the similarities:

http://www.answersingenesis.org/articles/am/v2/n2/flood-legends [answersingenesis.org]