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19 new pieces of non-human DNA have just been discovered lurking between human genome. This DNA was inherited by viruses that first infected our ancestors hundreds of thousands of years ago.

A study published in the Proceedings of the National Academy of Sciences, studied the DNA of 2500 people. In the DNA of 50 people scientists found a stretch of new DNA, which contained an intact, full genetic recipe for an entire virus. However, it is yet unknown if the newfound DNA can replicate, or reproduce but different studies of ancient virus DNA have demonstrated that it affects the humans who carry it.

In addition to finding these new stretches, the scientists also confirmed 17 other pieces of virus DNA found in human genomes by other scientists in recent years.

The study looked at the entire span of DNA, or genome, from different people around the world, including a large number from Africa, where the ancestors of modern humans originated before migrating around the world. Sophisticated techniques were used to compare key areas of each person's genome to the "reference" human genome.

The study was done at Tufts University and the University of Michigan Medical School and it was funded by the National Institutes of Health (NIH).

Findings of HERV

HERVs or endogenous retroviruses are ancient infectious viruses that inserted a DNA-based copy of their own RNA genetic material into our ancestors' genomes. They're part of the same type of virus that includes the modern human immunodeficiency virus, which causes AIDS.

Over generations, the virus-generated DNA kept getting copied and transmitted when humans reproduced. That's how it ended up in our DNA today. In fact, about 8% of what is thought of as "human" DNA actually was inherited from viruses. In some cases, human body has adopted the HERV sequences for useful purposes, such as one that helps a pregnant woman's body to form a cell layer around a developing fetus to protect it from toxins that are found in mother’s blood.

The new HERVs belong to the family called HERV-K. The intact whole viral genome, or provirus, that was recently discovered is the second one12966054_1194124670599260_1544445862_n

In the researcher's own words: "This one looks like it is capable of making infectious virus, which would be very exciting if true, as it would allow us to study a viral epidemic that took place long ago," says senior author and virologist John Coffin, Ph.D. of the Tufts University School of Medicine. "This research provides important information necessary for understanding how retroviruses and humans have evolved together in relatively recent times."

"Many studies have tried to link these endogenous viral elements to cancer and other diseases, but a major difficulty has been that we haven't actually found all of them yet," says co-first author Zachary H. Williams, a Ph.D. student at Tufts University in Boston. "A lot of the most interesting elements are only found in a small percentage of people, which means you have to screen a large number of people to find them."

"This is a thrilling discovery. It will open up many doors to research. What's more, we have confirmed in this paper that we can use genomic data from multiple individuals, compared to the reference human genome to detect new HERVs. But this has also shown us that some people carry insertions that we can't map back to the reference" says co-first author Dr. Julia Wildschutte.

The genetics researcher Dr. Jeffrey Kidd at the University of Michigan worked with Wildschutte when she was a member of his laboratory team. "These are remnants of ancient events that have not been fixed in the population as a whole, but rather happened in the ancestors of some people alive today," Kidd says. "There have been a number of examples of other HERVs that insert themselves next to human genes or near them, and have impact on their expression. We're interested in applying these methods to find other types of viral or mobile element insertions."

Genomic analysis

Dr. Kidd and her team have developed methods for characterizing repetitive DNA sequences which were used in this study, while Coffin and Williams used complementary techniques. They examined a set of genomes which was obtained from the international collaboration with 1000 Genomes Project. A different set of genomes examined, was acquired from the Human Genome Diversity Project which was done by Kidd and her colleagues at Stanford University. The latter set was focused on DNA samples from African volunteers and showed more signs of HERVs, in line with the high level of genetic diversity in African populations. That diversity stems from the longtime stability and intermixing of the continent's population as opposed to other populations in Europe, Asia and the Americas that stem from specific out-migrations in ancient times.

Cataloging all the HERV insertions in humans will require even more scanning of whole human genomes, which are becoming easier to come by as technology improves and becomes less expensive. And although intact proviruses lurking in our DNA may be rare, the impact of other HERV sequences on our health or disease is probably not.

References

  • University of Michigan Health System. "More ancient viruses lurk in our DNA than we thought." ScienceDaily. ScienceDaily, 22 March 2016.
  • Julia Halo Wildschutte, Zachary H. Williams, Meagan Montesion, Ravi P. Subramanian, Jeffrey M. Kidd, John M. Coffin. Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proceedings of the National Academy of Sciences, 2016; 201602336 DOI:10.1073/pnas.1602336113
  • www.sciencedaily.com/releases/2016/03/160322100714.htm
  • https://now.tufts.edu/news-releases/more-ancient-viruses-lurk-our-dna-we-thought-0
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