Comments on: Bornavirus DNA in the mammalian genome

By: profvrr

profvrr — Tue, 03 Aug 2010 01:36:57 +0000

The filovirus DNA is integrated into the mouse and rat genome at the
same position. The most likely explanation is that the DNA was
inserted into the evolutionary predecessor of the mouse and rat. Since
this lineage split about 40 million years ago, it provides a minimum
estimate for the age of the integration event at which time the virus
was also present.

By: gsgs

gsgs — Mon, 02 Aug 2010 23:59:21 +0000

40M years ago ? I wonder how they determined that.
Would you recognize a virus after 40M years or even 40K years ?
It may change properties like killing cells or even convert from
RNA-virus to retrovirus

By: Ed

Ed — Wed, 20 Jan 2010 22:12:42 +0000

Regarding other viral DNA in cells there are two genes, AngRem52 and 104 I believe, that were previously ascribed to the human genome but BLAST searches by two independent virus groups turned up matches to Paramyxoviridae. Both articles discuss where this DNA might have come from:
In silico identification of a putative new paramyxovirus related to the Henipavirus genus.
Schomacker H, Collins PL, Schmidt AC.
Virology. 2004 Dec 5;330(1):178-85.

A novel paramyxovirus?
Basler CF, García-Sastre A, Palese P.
Emerg Infect Dis. 2005 Jan;11(1):108-12.

By: Ed

Ed — Wed, 20 Jan 2010 14:12:42 +0000

By: I'll see your bornaviruses, and raise with a poxvirus | Mystery Rays from Outer Space

Fri, 15 Jan 2010 14:35:18 +0000

[...] });Original paper in Nature[↩]See commentary in the New York Times; the Virology Blog; and Not Exactly Rocket Science[↩]The Nasonia Genome Working Group (2010). Functional and [...]

By: Bo Liang

Bo Liang — Fri, 15 Jan 2010 02:54:18 +0000

I think it is also important to determine whether the integration sites are the same among different individuals. If so, then we may conclude that it arise from very very ancient time. If not, it would be even more interesting.

By: Tweets that mention Bornavirus DNA in the mammalian genome -- Topsy.com

Tweets that mention Bornavirus DNA in the mammalian genome -- Topsy.com — Thu, 14 Jan 2010 07:20:09 +0000

[...] This post was mentioned on Twitter by Vincent Racaniello, Chris Upton and Khader Shameer, I Andrade. I Andrade said: RT @profvrr: Bornavirus DNA in the mammalian genome http://bit.ly/5VM2r7 at virology blog [...]

By: uberVU - social comments

uberVU - social comments — Thu, 14 Jan 2010 03:00:21 +0000

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By: profvrr

profvrr — Thu, 14 Jan 2010 00:21:00 +0000

As for other viruses – DNA could be in cells as long as they don’t kill the cell, obviously. That rules out a lot of RNA viruses including flu. But who knows – maybe in a certain cell type infection is persistent for many acute viruses.

Fifty thousand years comes from calculating back based on the annual rate of change. It’s been bothering evolutionary virologists for some time. See this paper for more information on this: http://jvi.asm.org/cgi/content/full/77/7/3893?view=long&pmid=12634349

By: profvrr

profvrr — Wed, 13 Jan 2010 21:22:30 +0000

As for other viruses - DNA could be in cells as long as they don't kill the cell, obviously. That rules out a lot of RNA viruses including flu. But who knows - maybe in a certain cell type infection is persistent for many acute viruses.

Fifty thousand years comes from calculating back based on the annual rate of change. It's been bothering evolutionary virologists for some time. See this paper for more information on this: http://jvi.asm.org/cgi/content/full/77/7/3893?v...

By: poxdoc

poxdoc — Wed, 13 Jan 2010 19:19:18 +0000

Nice blog. I haven't read the paper.

Yes I was thinking about this this morning and thinking that viruses probably economize more than cells, thus carry less junk. However, pox genomes carry quite a few broken genes. I don't know the timeline for these, but it's clear that the viruses can carry apparently useless stuff around for quite a while. There's even a poxvirus that has an inserted retrovirus! So as we've already discussed, my prejudice for a long time has been that cells carry a lot of pure junk or broken genes or lame backups or even blank tape.

It's nice to have the borna sequences to give a new date to viruses. I don't understand where the 50,000 year birth date comes from for RNA viruses. Is this a phony number resulting from rapid evolution? I've always figured that viruses and cells have co-evolved from the get-go so that they would be a similar age. Could be viruses even predate cells in the primordial soup.

And is borna (or arena) virus special in doing this or have we just not looked hard enough, as you discuss in TWiV 65? I'll bet that if anyone were to look hard enough they would find evidence for this for just about any virus. I would bet it would maybe be more common for viruses that do an abortive or persistent infection in humans, maximizing the chances of fixing an event. And how do we know that the sequences came from borna and not the other way around? (The paper may address this but as I said I've not read it.)

Cool stuff. TWiV rocks.

By: Tyler

Tyler — Wed, 13 Jan 2010 16:40:55 +0000

"Perhaps the most intriguing question is the role of endogenous viral elements in the mammalian chromosome. It was previously known that 8% of the human genome is made up of endogenous retroviruses, and the human LINE-1 retrotransposon comprises 20% of human DNA. In my view, such sequences must have a functional role, or they would not have been maintained in the genome for millions of years. They are known to affect the human genome by causing insertion mutations and genomic instability, and by altering gene expression."

You don't actually have to invoke functional roles for the bulk of LINE-1 element insertions in the human genome to explain their presence. As selfish DNA they encode the ability to replicate themselves and create new insertions, although most of the LINE-1 elements in the human genome are inactive due to mutations in their open reading frames or are truncated due to their particular mechanism of insertion. Most of the elements can't actually move anymore and a great deal of them are probably selectively neutral at the level of the host genome and therefore there is little impetus for natural selection to remove them. So they just sit and accumulate mutations.

Some LINE-1 insertions may have become useful to the host, a process known as exaptation. For instance, close to 79% of all human genes contain at least a partial LINE-1 insertion, most of which are in introns. It was found a few years ago that the presence of these insertions might modulate the transcription of certain genes, because the transcriptional machinery seems to recognize LINE-1 sequence and slow down or stop transcription prematurely. Highly expressed genes were found to have less LINE-1 insertions and more lowly expressed genes were often found to have far more. These insertions occurred due to the selfish nature of LINE-1 elements but they may have been retained where they are because at that particular spot they are useful to the host. It doesn't mean that other LINE-1 elements aren't selfish or junk DNA, it just means these particular insertions are useful.

Han, J.S., S.T. Szak, and J.D. Boeke. 2004. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429: 268-274.