200,000 ERVs...

[RichardT]

The Pan troglodytes genome can be found here:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=13184

Thank you. I didn't notice that you replied.

 

[RichardT]

OK. I found an orthologous ERV on chromosome 1.

Description / Class / Family
LTR55 / LTR / ERV
LTR55[2] / LTR / ERV


I don't know if I'm looking properly though. There seems to be way more ERVs on the chimp genome than on the human genome.

Never mind. I know what I did wrong. I shall continue when I get back. I can spend hours doing this.

 

[TheOutsider]

*bump*

 

[Loudmouth]

OK. I found an orthologous ERV on chromosome 1.

Description / Class / Family
LTR55 / LTR / ERV
LTR55[2] / LTR / ERV


I don't know if I'm looking properly though. There seems to be way more ERVs on the chimp genome than on the human genome.

Never mind. I know what I did wrong. I shall continue when I get back. I can spend hours doing this.

Like I said, my area of expertise is protein chemistry so I am hoping that sfs can stop by and clear up any misconceptions.

With that in mind, it appears that neither genome is fully annotated. Annotation is the process of looking at the code and determining it's mostly likely origin and function. This takes time. For support of my hypothesis on incomplete annotation, search for "ERVL" on the human genome search page. There are over 200 hits but they only occur on three chromosomes. I really doubt that ERV-L insertions are really limited to three chromosomes, but I could be wrong.

The human genome paper used a program that can detect repeat sequences in the genome. They didn't go through base by base and label them. I am not sure how, specifically, the authors in the chimp genome paper compared ERV's. Since sfs is an author on the paper perhaps he could chime in.

 

[RichardT]

Since sfs is an author on the paper perhaps he could chime in.

Wow. Really.

 

[alloytoo]

Captured a print screen for table 11 from the human genome paper. It is attached below.

My memory was a little off. Solo LTR's are not listed separately, but ERV's still make up about 4.5% of the human genome and there are 203,000 of them. The first column lists the number of copies (x 1,000).

Hi Loudmouth.

I've recently followed this debate with interest, and found the evidence fascinating.

The notion that ERV insertions provide a history of life is extremely powerful.

I've also been following the debate on PtERV insertions and the posible implications for HIV research. fascinating stuff.

My understanding (correct me if I'm wrong and forgive me if I'm repeating the obvious)

Both Chimps and Humans have about 200000 ERV insertions, most of those insertions are orthologous (in the same place). IE: they happened in the more distant past to a shared ancester (>5-7Million years ago) more recent one are unique or non orthologous. (Non - Orthologous, IE we share them, but from horizontal transfer, rather than Linear.)

Unique, either only humans have them, or only Chimps have them.

PtERV is unique (sort of, other great apes also have them) as humans don't.

PtERV is Non-orthologous amongst those great apes.

It's presence in more than one species is suggestive of horizontal transfer, this is supported by evidence that shows Orangutans and new world monkey's (seperated by geography) don't have PtERV either.

Which leaves humans the odd ape out. We were present in africa along with Chimps and Gorilla's but somehow resisted the infection. That resistance may be at the expense of vulnerability to HIV, while chimps are seemingly immune to SIV?

Phew I hope that made sense.

My question however is simply this, using tables 2 & 11, how do you derive your figure of 200000 ERV insertions.

Assume I'm an idiot, the accountant in me just wants to add the columns, but that clearly doesn't work.

ERV insertions are such compelling evidence, I want to understand the number and refer to it as evidence.

Thanks for your time.

 

[Loudmouth]

My understanding (correct me if I'm wrong and forgive me if I'm repeating the obvious)

Both Chimps and Humans have about 200000 ERV insertions, most of those insertions are orthologous (in the same place). IE: they happened in the more distant past to a shared ancester (>5-7Million years ago) more recent one are unique or non orthologous. (Non - Orthologous, IE we share them, but from horizontal transfer, rather than Linear.)

Orthologous ERV's inserted before the chimp and human lineages diverged. I think this is a much better way of picturing it.

For humans and chimps specifically, both chimps and humans have orthologous AND non-orthologous ERV-K insertions. This retrovirus was active before and after the human and chimp lineages diverged which explains why we see orthologous and non-orthologous ERV-K insertions.

For PtERV's we no orthologous insertions. This retrovirus infected several different primate species independently.

As an aside, it might be interesting to see if there are chimp and bonobo specific PtERV insertions.

Unique, either only humans have them, or only Chimps have them.

It's [PtERV] presence in more than one species is suggestive of horizontal transfer, this is supported by evidence that shows Orangutans and new world monkey's (seperated by geography) don't have PtERV either.

It is the orthologous or non-orthologous nature of the ERV's which suggest horizontal or vertical transfer. It is very concievable that a retrovirus will infect different great apes but not all of them. However, independent insertions will not produce orthologous insertions given the fact that all known retroviruses insert randomly among thousands of insertion sites.

Which leaves humans the odd ape out. We were present in africa along with Chimps and Gorilla's but somehow resisted the infection. That resistance may be at the expense of vulnerability to HIV, while chimps are seemingly immune to SIV?

I have heard something to that effect, but I haven't researched it. It is an interesting hypothesis that might be worthy of a new thread.

My question however is simply this, using tables 2 & 11, how do you derive your figure of 200000 ERV insertions.

Table 11 from the human genome paper lists the total number of human ERV's. Five years later the chimp genome paper came out and the obvious thing to do is compare the chimp genome to the human genome, which is what they did. Table 2 from the chimp genome paper cuts to the chase. It lists the human specific and chimp specific ERV's. If you want to know how many ERV's the chimp genome contains you take the number of human ERV's, subtract the human specific ERV's (i.e. the non-orthologous ERV's), and add the chimp specific ERV's. Voila, you arrive at the ERV content of the chimp genome.

 

[Blayz]

That resistance may be at the expense of vulnerability to HIV, while chimps are seemingly immune to SIV?

it is unlikely the presence or absence of ERVs has any affect on susceptibility to other retrovirus infections. There are many different strains of SIV, each of which infects its own monkey/ape. generally speaking, a strain from a particular animal causes no disease in that animal, but does if it infects another, so for example chimp SIV doesn't cause disease in chimps but does in Macaques.

SIV does not infect humans, but HIV-1 and HIV-2 are derived from different strains of SIV (from different monkeys). HIV does not cause disease in chimps.

Scientists also work with a chimeric strain (partly SIV, partly HIV) called SHIV.

 

[gamespotter10]

so, we really share 200,000 ERV sequences with chimps which are in the same place in human and chimp genomes?

 

[RichardT]

so, we really share 200,000 ERV sequences with chimps which are in the same place in human and chimp genomes?

I don't know.

http://foru.ms/t5784958

 

[Loudmouth]

so, we really share 200,000 ERV sequences with chimps which are in the same place in human and chimp genomes?

Judging from the papers I have read the answer is yes.

 

[gamespotter10]

Judging from the papers I have read the answer is yes.

wow. thats like winning the lottery wherein there are 10 billion times as many people living on earth and everyone takes part in it

1 in 5x10^20 since there are at minimum 50 million different places the ERV can insert itself

 

[SLP]

On the futility of 'debating' technical issues with Mrk Kennedy:

http://all-too-common-dissent.blogspot.com/2006/02/for-mark-kennedy.html

 

[TheOutsider]

*bump*

 

[alloytoo]

Table 11 from the human genome paper lists the total number of human ERV's. Five years later the chimp genome paper came out and the obvious thing to do is compare the chimp genome to the human genome, which is what they did. Table 2 from the chimp genome paper cuts to the chase. It lists the human specific and chimp specific ERV's. If you want to know how many ERV's the chimp genome contains you take the number of human ERV's, subtract the human specific ERV's (i.e. the non-orthologous ERV's), and add the chimp specific ERV's. Voila, you arrive at the ERV content of the chimp genome.

Thanks, I've obviously been incredible dense in reading those tables.

I must save I can't see how anyone can consider those figures and not conclude common descent.

Discussions around PtERV and CERV2 are all very interesting, and one can speculate ad nausea about why human don't have them, and Chimps and Gorilla's have them at non-Orthologous positions, but really it makes absolutely no difference to the the ultimate conclusion that Chimps and Humans share a vast common ancestry.

 

[alloytoo]

it is unlikely the presence or absence of ERVs has any affect on susceptibility to other retrovirus infections. There are many different strains of SIV, each of which infects its own monkey/ape. generally speaking, a strain from a particular animal causes no disease in that animal, but does if it infects another, so for example chimp SIV doesn't cause disease in chimps but does in Macaques.

SIV does not infect humans, but HIV-1 and HIV-2 are derived from different strains of SIV (from different monkeys). HIV does not cause disease in chimps.

Scientists also work with a chimeric strain (partly SIV, partly HIV) called SHIV.

What I meant was, that the existance, or non existance or certain ERV is an indicator of what we (as a species) were immune to, which may have come at a price of current vulnerabilities.

 

[Blayz]

What I meant was, that the existance, or non existance or certain ERV is an indicator of what we (as a species) were immune to, which may have come at a price of current vulnerabilities.

Right, the answer is no. The presence of ERV sequences says nothing about our immunity, and thus nothing about our vulnerabilities.

 

[alloytoo]

Right, the answer is no. The presence of ERV sequences says nothing about our immunity, and thus nothing about our vulnerabilities.

A history of past infections so severe that they become part of our genetic code compared with our closest related species and their history of past infections, tells us nothing about our species possible immune responses?

 

[Blayz]

A history of past infections so severe that they become part of our genetic code compared with our closest related species and their history of past infections, tells us nothing about our species possible immune responses?

1) Retroviral insertion is not a measure of severity. There are many diseases that will kill you dead and don't go near your genome.

2) "immunity" by definition, means you don't get the infection. So you are asking about viruses that no longer exist that didn't insert into the genome.

3) Most retroviral/natural host infections are asymptomatic, ie the host doesn't know it has the infection. This is not the same as being immune.

4) the adaptive, and indeed innate immune responses are not related to whether the pathogen integrates.

 

[alloytoo]

1) Retroviral insertion is not a measure of severity. There are many diseases that will kill you dead and don't go near your genome.

2) "immunity" by definition, means you don't get the infection. So you are asking about viruses that no longer exist that didn't insert into the genome.

3) Most retroviral/natural host infections are asymptomatic, ie the host doesn't know it has the infection. This is not the same as being immune.

4) the adaptive, and indeed innate immune responses are not related to whether the pathogen integrates.

That doesn't mean it tells us NOTHING.

It tells us something that must be taken in context.