Huge swaths of our DNA library are made-up of non-coding genes that were long considered “junk DNA”. Recent findings, however, shown these bits of DNA actually have many purposes in mammals.
Some help form the structure in our DNA molecules, in order that they can be packaged neatly within our cell nuclei, while others are involved in gene regulation.
Now, researchers from the University of latest South Wales in Australia discovered another potential purpose for these non-coding instructions, within the genomes of marsupials.
Some of the gene sequences once considered “junk” are actually fragments of viruses left buried, in our DNA from an infection in a long-forgotten ancestor.
Whenever a virus infects you, there is a chance it’ll leave behind a piece of itself within your DNA and if this happens in an egg or sperm, it’ll then be passed on through the generations. These are referred to as Endogenous Viral Elements (EVEs).
In humans, fragments of viral DNA structure around 8% of our genome. They can provide a record of viral infections through our evolutionary history, just like genetic memory.
“These viral-fragments have been retained for a reason,” said paleovirologist Emma Harding. “Over millions of years of evolution, we might expect all DNA to change, however, these fossils are preserved & kept intact.”
To try to work-out why, Harding & colleagues looked for EVEs in the genomes of 13 species of marsupials, including the tammar wallaby (Macropus eugeni), Tasmanian devil (Sarcophilus harrisii), & fat-tailed dunnarts (Sminthopsis crassicaudata).
They found EVEs from 3 viral groups, Bornaviridae, Filoviridae & Parvoviridae, in all of the animals sampled.
“One of the EVEs I found was from the Bornaviridae family of viruses, which first entered the animal’s DNA during the time of the dinosaurs when South American & Australian land masses were still joined together,” Harding said. Bornaviridae is present in the opossums of America also as Australia’s marsupials.
The Bornaviridae EVEs were particularly prevalent & more closely associated with similar viral fossils found in birds & reptiles, instead of, those seen in placental mammals like us.
“Bornaviridae viruses were previously thought to have evolved 100-million years ago,” Harding explained. “But the one I found in almost every marsupial DNA, we looked at puts it at 160 million years old.”
Surprisingly, a number of these ancient viral fragments were still being transcribed into RNA. Often in cells, RNA transcription act as protein templates. But in this case, they were not being translated, effectively making them non-coding RNA.
That does not make them useless. Non-coding RNA is used in most of cell functions, including the regulation of RNA transcription among other genes.
Significantly, it’s also known that this sort of RNA is used for several cell functions, including regulating the creation of RNA and it’s also known to contribute to immune defense against viruses in plants & invertebrates.
Bats have a particularly large cache of those fossil viral fragments too and they are well known for their unfortunate ability to survive, while carrying deadly viruses that do most other mammals in.
Looking at koalas in additional detail, researchers discovered a number of the EVEs were indeed being transcribed into small RNA molecules, known to be antiviral in invertebrates.
“This suggests the tantalizing possibility of this RNA defense system, previously thought to be abandoned in mammals in favor of interferon system, still being active & protecting marsupial cells,” Harding & colleagues wrote in Microbiology Australia.
As marsupials undergo much of their developmental time within their mother’s pouch, some are born before they have even developed bones let alone fully functioning immune systems. So, this type of antiviral defense could be critical to pouch young, the team suspects.
“This could be a mechanism similar to vaccination but is inherited through generations. By keeping a viral fossil, cell is immunized against future infection,” said Harding.
“If we will show it occurring in marsupials, it may be occurring in other animals, including humans.”
This research was published in Virus Evolution.