100,000 viruses hid in human genes (endogenous retroviruses )

Virus epidemic within our genome

Scientists have uncovered clues as to how mammal genomes became riddled with viruses. The research reveals important information about the so-called 'dark matter' of the human genome.

For years scientists have been struggling with the enigma that more than 90 percent of every mammal's genome has no known function. A part of this 'dark matter' of genetic material is known to harbour pieces of DNA from ancient viruses that infected our ancestors going back as far as the age of the dinosaurs.

(G. Magiorkinis, R. J. Gifford, A. Katzourakis, J. De Ranter, R. Belshaw. Env-less endogenous retroviruses are genomic superspreaders. Proceedings of the National Academy of Sciences, 2012; DOI: 10.1073/pnas.1200913109)

(http://www.sciencedaily.com/releases/2012/05/120501210558.htm)

A virus hid in our genome for six million years

In the mid-2000s, David Markovitz, a scientist at the University of Michigan, and his colleagues took a look at the blood of people infected with HIV. Human immunodeficiency viruses kill their hosts by exhausting the immune system, allowing all sorts of pathogens to sweep into their host’s body. So it wasn’t a huge surprise for Markovitz and his colleagues to find other viruses in the blood of the HIV patients. What was surprising was where those other viruses had come from: from within the patients’ own DNA.

Scientists have identified 100,000 pieces of retrovirus DNA in our genes, making up eight percent of the human genome. That’s a huge portion of our DNA when you consider that protein coding genes make up just over one percent of the genome.

Close-up on HIV. Voth Lab, University of Chicago. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2966041/

Scientists have studied these so-called endogenous retroviruses both in humans and in other species, and the evidence all points to the same scenario for how they genetically merged with us. Our ancestors were infected with retroviruses on a regular basis. On rare occasion, a virus infected a sperm or egg and managed to end up in an embryo. Every new cell in the embryo inherited the retrovirus DNA implanted in its genome. And then the embryo grew up into an adult, which then had offspring of its own, and passed the virus DNA on as well.

(Carl Zimmer:  http://phenomena.nationalgeographic.com/2013/05/10/the-lurker-how-a-virus-hid-in-our-genome-for-six-million-years/)
Retroviridae is a family of enveloped viruses that replicate in a host cell through the process of reverse transcription. A retrovirus is a single-stranded RNA virus that stores its nucleic acid in the form of an mRNA genome (including the 5' cap and 3' PolyA tail) and targets a host cell as an obligate parasite. Once inside the host cell cytoplasm the virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome, the reverse of the usual pattern, thus retro (backwards). This new DNA is then incorporated into the host cell genome by an integrase enzyme, at which point the retroviral DNA is referred to as a provirus. The host cell then treats the viral DNA as part of its own genome, translating and transcribing the viral genes along with the cell's own genes, producing the proteins required to assemble new copies of the virus. It is difficult to detect the virus until it has infected the host. At that point the infection will last forever. (http://en.wikipedia.org/wiki/Retrovirus)

Endogenous retroviruses (ERVs) are endogenous viral elements in the genome that closely resemble and can be derived from retroviruses. They are abundant in the genomes of jawed vertebrates and they occupy as much as 4.9% of the human genome. ERVs are a subclass of a type of gene called a transposon which is able to be packaged and moved within the genome to serve a vital role in gene expression and regulation. Research shows that retroviruses have evolved from a type of transposable gene called a retrotransposon which includes ERVs; these genes can mutate and instead of moving to another location in the genome they can became exogenous/pathogenic. This means that all ERVs may not have originated as an insertion by a retrovirus but rather some may have been the source of origin for the genetic information in the retroviruses they resemble.
(http://en.wikipedia.org/wiki/Endogenous_retrovirus)
Genetic evidence for common descent: We have found that primates share many nearly identical ERVs. The only explanation for this is common descent: a common ancestor of all primates had the ERV and thus passed it on. In fact, scientists can build a tree of relationships using ERVs (on the left) that fits perfectly with evidence from other fields. There is, quite simply, no other explanation for these similar ERVs besides common descent.
(http://phylointelligence.com/genetics.html)

 Eight percent of human genetic material comes from a virus

About eight percent of human genetic material comes from a virus and not from our ancestors, according to a new study. The research shows that the genomes of humans and other mammals contain DNA derived from the insertion of bornaviruses, RNA viruses whose replication and transcription takes place in the nucleus.

A new study shows that the genomes of humans and other mammals contain DNA derived from the insertion of bornaviruses, RNA viruses whose replication and transcription takes place in the nucleus.

 (http://www.sciencedaily.com/releases/2010/01/100107103621.htm)
Genetic evidence for common descent: We know this because mammals, especially primates, share several of these BDV insertions with humans. The chance of highly similar viral elements being inserted into the same regions in the genome of different organisms independently is extraordinarily low. This is where evolution comes in: the explanation for this becomes obvious when one realizes that mammal taxa share these viral elements because they share a common ancestor.
(http://phylointelligence.com/genetics.html) 

1. Masayuki Horie, Tomoyuki Honda, Yoshiyuki Suzuki, Yuki Kobayashi, Takuji Daito, Tatsuo Oshida, Kazuyoshi Ikuta, Patric Jern, Takashi Gojobori, John M. Coffin & Keizo Tomonaga. Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature, 2010; 463 (7277): 84 DOI: 10.1038/nature08695
2. Cédric Feschotte. Virology: Bornavirus enters the genome. Nature, 2010; 463 (7277): 39 DOI: 10.1038/463039a

Who is really in charge 
of this body of ours..

It also makes me wonder who is really in charge of this body of mine — me or the viruses that inhabit it? Do I have free will or am I behaving the way my viruses want me to? It’s starting to feel like viruses are calling all the shots when you get down to the bottom of things. There’s a science fiction movie script here for someone.(Judy/May14,2013/NatGeo)

That collection of organisms that is you is most likely guided by “cooperative viruses” rather than selfish genes free will – not a chance.on Byrd/May15,2013/NatgGeo)(D