Scientists discover new roles for viral genes in the human genome

March 5, 2015 by Winnie Lim

Research on the expression of viral DNA within the human genome furthers our understanding of human evolution and embryonic development

Singapore – The human genome is the blueprint for human life, but much of this blueprint still remains a mystery. Researchers from A*STAR's Genome Institute of Singapore (GIS) have now discovered that sequences from old viruses that were thought to be useless, might contribute to the earliest cell types in the human life cycle. These newly discovered viral elements can be used to identify new types of embryonic stem cells, opening more possibilities to understanding and diseases.

The viral sequences that are the focus of the discovery are similar to retroviruses , but since they are a part of the human genome, they are known as endogenous retroviruses (ERV). ERVs are able to reinsert another copy of their own DNA into the human genome once they are activated. Since they mainly multiply their own DNA, they are sometimes referred to as 'selfish DNA'. Because of their 'selfishness', ERVs are potentially dangerous when they destroy genes that are essential to human life. In a study recently published in Cell Stem Cell, scientists describe that many ERVs are activated in cells from early embryos, but instead of being harmful, they might have become useful over the course of evolution.

Genes that are activated are transcribed into RNA to function. Therefore, scientists investigate the RNAs in the cell to identify active genes. "When we investigated public data from , we found that many RNAs originated from regions in the human genome that are ERVs," explained GIS Fellow Dr Jonathan Göke, who led the study. "We did not only observe isolated events, but systematic activation of these ERVs. Every cell type showed transcription of specific classes, something that is very unlikely to occur by chance".

"Many ERV elements are only fragments of the full viruses," added Dr Göke. "They maintain the activation sequence, but the RNA that they generate can be very different from the RNA that retroviruses generate". In many cases, these ERV-RNAs are even parts of RNAs generated from other genes. This way, ERVs might have evolved to gain a new function; they might have become a part of the blueprint for human life.

ERVs have been shown to play a role in diseases such as cancer. Because many ERVs are not expressed in the most widely used cell models, and they do not exist in mouse, scientists do not yet fully understand their function. The researchers now showed that a part of the ERVs which functions as activator can be used to identify cells that show expression of these ERV families. Such cells might overcome the limitations of current cell models to study the role and function of ERVs in development and disease.

"These are fascinating findings as the embryonic cells that express these ERV-derived RNAs are fundamental to the human life cycle. Now the big question is what they are actually doing." said Dr Guillaume Bourque, associate professor at the McGill University in Canada, who has worked on ERVs himself for many years. "From research with human , we know that ERVs have become essential, so it is quite likely that the ERVs described in this study contribute in a number of ways to human development."

"This is a very exciting study," said Prof Huck-Hui Ng, executive director of the GIS. "The results open up many new opportunities to better understand why and how embryonic cells are different from adult cells, and what role these newly discovered ERV-genes play. Some ERVs may even be involved in the formation of diseases, such as cancer."

Dr Göke's team at the GIS plans to take their research further. "We are now developing new algorithms that will help us identify additional ERVs in the , and we try to isolate that express these ERV-RNAs. This way we will be able to study their function and how they contribute to human diseases".

Explore further: New knowledge about host-virus coevolution unmasked from the genomic record

More information: "Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells." DOI: dx.doi.org/10.1016/j.stem.2015.01.005

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JVK
1 / 5 (3) Mar 05, 2015
See for comparison the representation of nutrient-dependent pheromone-controlled ecological adaptation of a new human species in Greg Bear's presentation: https://www.youtu...NcMR_-RU

Or, see the more technical representation from my 2013 poster session
Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation) https://www.youtu...youtu.be

Viral microRNAs and nutrient-dependent microRNAs link the anti-entropic epigenetic effects of nutrients to the pheromone-controlled fixation of amino acid substitutions that differentiate cell types in all cells of all individuals of all species via the biophysically constrained chemistry of protein folding. The balance of viral microRNAs and nutrient-dependent microRNAs ensures that entropic elasticity leads to the optimal stability of DNA in organized genomes.
JVK
1 / 5 (3) Mar 05, 2015
Nutrient stress and social stress lead to perturbed protein folding via mutations linked to physiopathology -- except in explanations by theorists who know nothing about physics, chemistry, or conserved molecular mechanisms.

They think there are beneficial mutations that can somehow be linked to the evolution of biodiversity as if perturbed protein folding could link one species to the mutation-driven evolution of increasing organismal complexity in another species.
RealScience
5 / 5 (4) Mar 05, 2015
The biologically uninformed continue to yell: MUTATIONS! (JVK, DEC 18, 2014)



I'll let your own words do the talking, JVK, since you have YET AGAIN introduced that term to a thread.

LMAO!
anonymous_9001
5 / 5 (4) Mar 05, 2015
Nutrient stress and social stress lead to perturbed protein folding via mutations linked to physiopathology


Which is the same thing that happens in mutagenesis studies. Templates are deliberately mutated with UV light, mutagenic PCR, or mutagenic chemicals to randomize them.
JVK
1 / 5 (4) Mar 05, 2015
...deliberately mutated with UV light, mutagenic PCR, or mutagenic chemicals to randomize them.


http://www.scribd...s#scribd
"Despite their challenges, ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered."

How can your meaningless results be meaningfully interpreted and linked to increasing organismal complexity, like these researchers just did?
anonymous_9001
5 / 5 (5) Mar 06, 2015
Get back on topic, Kohl.

Mutations are caused in mutagenesis experiments and improved enzyme function is the outcome after rounds of selection. It's that simple.
JVK
1 / 5 (3) Mar 06, 2015
...improved enzyme function is the outcome after rounds of selection.


Are you claiming that the improvements in enzyme function link mutations to the evolution of increasing organismal complexity.

If not, what are you claiming is a meaningful interpretation of your results?

I'm claiming that
"Viral microRNAs and nutrient-dependent microRNAs link the anti-entropic epigenetic effects of nutrients to the pheromone-controlled fixation of amino acid substitutions that differentiate cell types in all cells of all individuals of all species via the biophysically constrained chemistry of protein folding. The balance of viral microRNAs and nutrient-dependent microRNAs ensures that entropic elasticity leads to the optimal stability of DNA in organized genomes."

That's what this article is about: RNA-mediated cell type differentiation.
anonymous_9001
5 / 5 (4) Mar 06, 2015
Mutation and selection leading to increased function and complexity of ribozymes:

http://www.pnas.o...full.pdf

The observation that a ribozyme with novel catalytic function can arise from the structural foundation of a different ribozyme supports the concept that preexisting RNA structural domains in nature may have facilitated the evolution of more complex functional RNAs. This principle has been used to obtain ribozymes with polynucleotide kinase or ligase activity, starting from randomized pools of RNA molecules that contained a preexisting ATP-binding domain (34, 35), although in neither case was it clear whether the evolved catalysts continued to rely on the original ATP-binding domain. The results of the present study suggest that RNAs, like their protein counterparts, can be assembled from smaller domains to attain a higher level of structural and functional organization.
JVK
1 / 5 (3) Mar 06, 2015
1999
suggest that RNAs, like their protein counterparts, can be assembled from smaller domains


2011
If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based.
(p 1014)
http://jp.physoc....007.full

I'm claiming that
"Viral microRNAs and nutrient-dependent microRNAs link the anti-entropic epigenetic effects of nutrients to the pheromone-controlled fixation of amino acid substitutions that differentiate cell types in all cells of all individuals of all species via the biophysically constrained chemistry of protein folding. The balance of viral microRNAs and nutrient-dependent microRNAs ensures that entropic elasticity leads to the optimal stability of DNA in organized genomes."

What are you claiming that is based on what is currently known about physics, chemistry, and molecular biology?
anonymous_9001
5 / 5 (5) Mar 06, 2015
Joyce's papers since 2011:

http://scholar.go...ylo=2011
anonymous_9001
5 / 5 (5) Mar 06, 2015
Continuous In Vitro evolution of a ribozyme ligase: A model experiment for the evolution of a biomolecule (2013)

http://onlinelibr...abstract

189,000 results for "in vitro evolution" since 2011:

http://scholar.go...ylo=2011
JVK
1 / 5 (3) Mar 06, 2015
What are you claiming that is based on what is currently known about physics, chemistry, and molecular biology? See, for example:

Implicating microRNAs in cancer http://perfumingt...-cancer/

I'm claiming that you and other theorists are responsible for the suffering and death of millions of people, which is why others are now Combating Evolution to Fight Disease http://www.scienc...88.short

You seem to be fighting for suffering and death. Is that what they taught you to do at Carthage College?
anonymous_9001
5 / 5 (3) Mar 06, 2015
I'm claiming that you and other theorists are responsible for the suffering and death of millions of people, which is why others are now Combating Evolution to Fight Disease


You're taking that title out of context. It also helps to read past the title, like you seem to be doing.

Full text can be found here: http://www.ncbi.n...4117199/

From the 5th paragraph:

For example, in bacteria, responses to environmental stress can activate mutagenesis mechanisms that increase mutation rate


That's something I've been telling you for a long time.

Captain Stumpy
4 / 5 (4) Mar 07, 2015
You seem to be fighting for suffering and death. Is that what they taught you to do at Carthage College?
@jk
and so you continue to attack anyone with an education simply because you failed out of college and couldn't learn the basics
you should be flattered that someone is trying to teach you something

you STILL don't know the basics though
this is apparent above by your "interpretations" of an article based only upon it's title and little else
you obviously didn't read it as ANON points out[qFor example, in bacteria, responses to environmental stress can activate mutagenesis mechanisms that increase mutation rate want us to translate that or should we get the author to DEBUNK YOU again?

leave your religion at home, jk
there is NO ROOM in science for RELIGION
http://www.ploson...tion=PDF
JVK
1 / 5 (3) Mar 07, 2015
From the 5th paragraph:

For example, in bacteria, responses to environmental stress can activate mutagenesis mechanisms that increase mutation rate

That's something I've been telling you for a long time.


If true, that would show you must also know transgenerational responses to stress are nutrient-dependent and pheromone-controlled. That fact links the balance of viral microRNAs and nutrient-dependent microRNAS from RNA-directed DNA methylation and RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all species.

Why do you think other science idiots, like you, do not know that? Could it be due to the fact that you claimed "James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research. It was a mistake to let such a sloppy review through to be published." http://www.ncbi.n...4049134/
Bongstar420
1 / 5 (1) Mar 07, 2015
We had better ban GMO's and make sure that the acronym GMO is on every lable
JVK
1 / 5 (3) Mar 07, 2015
For intelligent comments about nutrient-dependent cell type differentiation in the context of the viral microRNA / nutrient-dependent microRNA balance and RNA-directed DNA methylation linked to the amino acid substitutions that differentiate the cell type of all individuals of all species, see:

Wrangling Retrotransposons http://www.the-sc...sposons/

Nourishing the Aging Brain http://www.the-sc...g-Brain/

Of Cells and Limits http://www.the-sc...-Limits/
RealScience
5 / 5 (4) Mar 08, 2015
@JVK - Your 'Wrangling Retrotransposons' citation links active L1 retrostransposons to aging and cancer. However of the more than 500,000 L1 copies in our genomes "most of these are inactivated as a result of mutation", and only roughly 100 "retain their ability to copy and paste themselves among the chromosomes, posing diverse dangers to our cells and possibly contributing to age-related deterioration."

So, JVK, YET AGAIN you have cited an article that shows that mutations CAN be beneficial...
JVK
1 / 5 (3) Mar 08, 2015
See: http://perfumingt...mit.y=13

Look at any of the ~200 blog posts at PerfumingtheMind.com They attest to how nutrient-dependent RNA-mediated events link amino acid substitutions to ecological adaptations via the pheromone-controlled physiology of reproduction in species from microbes to man.

Explain how mutations, which perturb protein folding, could replace biologically-based cause and effect, which is detailed in the context of everything currently known about the biophysically constrained chemistry of protein folding and RNA-mediated cell type differentiation that links the balance of viral microRNAs and nutrient-dependent microRNAs to the morphological and behavioral phenotypes of all genera.

If you explain how mutations lead to increasing organismal complexity, I will post your explanation to RNA-mediated.com when it goes live later this week.

I look forward to all ridiculous explanations.
RealScience
5 / 5 (3) Mar 09, 2015
I've seen far more than 200 of your comments on phys.org, JVK, so why would I go to your site to read the same repetitious drivel, mixed with interesting references that I have to explain to you, that you spam this site with?

As for:
.Explain how mutations ... RNA-mediated cell type differentiation that links the balance of viral microRNAs...


When a virus inserts DNA into our genome, that changes the nucleotide sequence of our DNA and is thus a mutation (as 'mutation' is generally used in genetics). Some viral DNA is transcribed into 'viral microRNAs', and you have already acknowledged a link between viral microRNAs and healthy cell type differentiation:
The co-transscriptional mechanisms involve viral microRNAs and nutrient-dependent microRNAs that typically lead to healthy nutrient-dependent cell type differentiation


What else do you need to have explained to you?
JVK
1 / 5 (3) Mar 09, 2015
What else do you need to have explained to you?


Same as always. Explain how mutations are beneficial to increasing organismal complexity so that they can be compared to the role of nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions in the context of controlled cell type differentiation.

...you have already acknowledged a link between viral microRNAs and healthy cell type differentiation...


No, that's what I have detailed in the context of an atoms to ecosystems model of how ecological variation leads to ecological adaptations in species from microbes to man -- without the pseudoscientific nonsense about mutations and ridiculous assumptions of how long it takes for them to accumulate and cause the evolution of a new species.
RealScience
5 / 5 (3) Mar 09, 2015
Same as always. Explain how mutations are beneficial to increasing organismal complexity

I just explained how the viral microRNAs you linked to healthy cell type differentiation originated from mutations, JVK.

Did you fail to read the explanation?
Or did you fail to understand the explanation?

Or are you claiming that 'viral microRNAs' are not related to viral sequences in our DNA?
Or are you claiming that a virus inserting DNA into our DNA is not a mutation?
(Since you don't say what you mean by mutation, I'm using the most standard definition in genetics).

Or are you claiming that you have not linked viral microRNAs to cell type differentiation?
Or are you claiming that healthy cell type differentiation is not beneficial to increasing organismal complexity?

Or other?

Please clarify what part of the explanation you either disagree with or do not to understand.
JVK
1 / 5 (3) Mar 09, 2015
...the viral microRNAs you linked to healthy cell type differentiation originated from mutations


I did NOT link the viral microRNAs to healthy cell type differentiation. I linked the nutrient-dependent microRNAs to healthy cell type differentiation.

You have once again shown that you are a biologically uninformed science idiot who is not capable of understanding the difference between mutations linked to physiopathology and nutrient-dependent RNA-mediated amino acid substitutions.

The substitutions link the epigenetic landscape to the physical landscape of DNA in species from microbes to man via conserved molecular mechanisms of the biophysically constrained chemistry of nutrient-dependent protein biosynthesis and degradation.
RealScience
5 / 5 (3) Mar 09, 2015
I did NOT link the viral microRNAs to healthy cell type differentiation. I linked the nutrient-dependent microRNAs to healthy cell type differentiation.


Then you need a course in writing clearly, because the following comments of yours sure do sound like linking viral micronRNAs to cell type differentiation:


This links viral microRNAs to cell type differentiation across species via the biophysically constrained chemistry of RNA-mediated protein folding.
(JVK, Feb. 5, 2015)

What do you think links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man? The serious scientists I know realize it is most likely viral microRNAs.
(JVK, Feb 21, 2015, and you have many times linked the physical landscape of DNA to cell type differentiation)

-continued-
RealScience
5 / 5 (3) Mar 09, 2015
-continued-

The co-transscriptional mechanisms involve viral microRNAs and nutrient-dependent microRNAs that typically lead to healthy nutrient-dependent cell type differentiation via the biophysically constrained chemistry of protein folding in species from yeasts to primates.
(JVK, Feb. 23, 2015)

This links viral microRNAs and nutrient-dependent microRNAs to changes in the microRNA/messenger RNA balance. Those changes link RNA-directed DNA methylation to RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of species.
(JVK, Mar. 2, 2015)

So which is it, JVK?
Are viral microRNAs BENEFICAL, leading to cell type differentiation and organismal complexity?
Or are viral microRNAs HARMFUL, interfering with nutrient-dependent micro-RNAs?
JVK
1 / 5 (4) Mar 09, 2015
You're not paying attention.

I've seen far more than 200 of your comments on phys.org, JVK,


http://rna-mediat...microRNA
Search Results for 'viral microRNA'

See also:
https://www.faceb...microRNA
RealScience
5 / 5 (3) Mar 10, 2015
Quit trying to evade the question, JVK.

Are viral microRNAs BENEFICAL, leading to cell type differentiation and organismal complexity?
Or are viral microRNAs HARMFUL, interfering with nutrient-dependent micro-RNAs?

Just give a straight answer so that anyone still reading this thread can see what you, JVK, now claim regarding whether viral microRNAs are beneficial or harmful.
RealScience
5 / 5 (3) Mar 11, 2015
Not answering, JVK?

The quoted comments of yours clearly implied a beneficial role for viral microRNAs. Since a virus inserting viral DNA into our genome is a mutation, that means that your comments acknowledge that some mutations are beneficial.

That's what happens when you incorporate buzz-words into your word-salad without understanding what they means, JVK.

JVK
1 / 5 (3) Mar 11, 2015
...that means that your comments acknowledge that some mutations are beneficial.


Who cares what a biologically uninformed science idiot thinks it means? No matter what anything actually means, they will twist the meaning into something else. That's what science idiots have always done.

"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another.... Assumptions, made but not verified, were taught as fact." http://www.huffin...211.html

One way to recognize a "RealScience" idiot is to watch as the idiot twists whatever anyone claims and suggests they are claiming something else.
RealScience
5 / 5 (3) Mar 11, 2015

Who cares what a biologically uninformed science idiot thinks it means? No matter what anything actually means, they will twist the meaning into something else. That's what science idiots have always done.
...
One way to recognize a "RealScience" idiot is to watch as the idiot twists whatever anyone claims and suggests they are claiming something else.


Your transference is acting up again, JVK...
You have been caught time and time again misinterpreting what published papers say and claiming that they say something else. The Captain and Anon have even contacted the authors to show that your claims are wrong.

I wouldn't be so impolite as to call you a 'Real Science Idiot', but if you really want to call yourself that, I won't disagree.
JVK
1 / 5 (3) Mar 12, 2015
http://rna-mediat...l-types/

RNA directed DNA methylation and cell types

Excerpt: These reports address the most recent work that links RNA-directed DNA methylation to RNA-mediated amino acid substitutions and cell type differentiation, which links the physiology of reproduction to the morphological and behavioral phenotypes of species from microbes to man.
RealScience
5 / 5 (2) Mar 12, 2015
@JVK - Since you posted a comment without insults, I looked at your blog.
It looks pretty much the same as your comments here.

You might want to fix your comment:
"They linked the immune system response to cell type differentiation in the viruses and cell type difference in the host across the course of the infection."

I'd be quite surprised if there was really 'cell type differentiation in the viruses', but that's what your comment sounds like you are saying...
JVK
2.3 / 5 (3) Mar 13, 2015
Thanks. I made the correction on both domains.

Are viruses microRNAs?
http://rna-mediat...crornas/
http://perfumingt...crornas/

"They linked the immune system response to viruses and cell type differences in the host across the course of the infection."

Captain Stumpy
3 / 5 (2) Mar 13, 2015
See: http://perfumingt...mit.y=13
ANY LINK to perfuming the mind is SPAM/TROLLING and NOT SCIENTIFIC
if you have a study there, link it from the original publication IF IT IS STILL VALID and not retracted
NOT your personal stinky perfume site
having a web site doesn't make you correct any more than having a penis makes you a porn star
No matter what anything actually means, they will twist the meaning into something else. That's what science idiots have always done
it is what YOU (jk) continue to do, as Real has just PROVEN

How many times have i or ANON also proven that you fail when you try to INTERPRET another study?
EVERY SINGLE TIME AN AUTHOR REPLIES!

that is 100% of EVERY TIME an author replied to us when queried about YOUR interpretations of their studies!!!!
HERE ON PO

http://www.ploson...tion=PDF

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