About a third of our DNA has been regarded as having no function. Now an Irish geneticist believes this 'junk' DNA may not be completely useless, writes Andrew Read
The genetic code that makes us what we are is contained within our DNA. Yet much of our DNA is not used to make anything. Why is it there? Many scientists have called it junk, but others have insisted it must do something. Dr Robin Allshire reports in Science magazine this week that this apparently functionless DNA can have its uses.
A large portion of the junk DNA in our bodies is believed to be derived from viruses known as retroviruses that have incorporated themselves into our genetic code, copied themselves and jumped about. This process probably accounts for as much as a third of all the DNA in our genome. These jumping elements are known as retrotransposons. They can cause havoc if they jump into the middle of an important gene, and so the body holds them carefully in check, says Dr Allshire. Very recent work has shown that these elements are "silenced" - that is, rendered inactive - by a process known as RNA interference.
But if they're junk, why not get rid of them? Some years ago, Dr Allshire showed that the chemistry of the silencing process can help hold chunks of DNA together during the process of cell replication. But now he has shown that this silencing process can also be used to silence normal genes that are near the "junk" DNA. Cells can therefore use their junk DNA to switch their genes off and on during development.
Dr Allshire, originally from Howth, Co Dublin, and a Genetics graduate from Trinity College Dublin, is now a Principal Research Fellow of The Wellcome Trust at Edinburgh University. For many years, he has been working with fission yeast, a common laboratory model for studying genetics. Its genome is smaller and simpler than ours, but the underlying genetic processes involved in cell division are believed to be similar. With Dr Vera Schramke in his laboratory at the Wellcome Trust Centre for Cell Biology at Edinburgh, Dr Allshire inserted a marker gene into fission yeast. They then experimentally induced RNA interference against this gene. Precisely the same machinery used by the cell to stop junk DNA doing anything also silenced this gene.
This raised the prospect that natural silencing processes directed at junk DNA could also be directed at important genes nearby. Using mutants with a defective silencing mechanism, or by putting active genes into regions of junk DNA, they showed that this was indeed the case. "This work definitely shows that junk DNA plays a role in the repression of neighbouring genes," said Dr Allshire.
The implication of all this is that DNA derived from ancient viral attack is now being used for an enforcing role on nearby genes. "Is this being done in a concerted manner, or is the cell just using what's around?" asks Dr Allshire. "We don't know. We need to look in related organisms and see if similar retrotransposon-derived DNA is used in similar places for the same job."
What of our own junk DNA? Relic retrotransposons constitute less than one per cent of the yeast genome, but over 30 per cent of ours. Is our extra junk used to control the presumably more complex development we have to undergo? Or is much of it true junk? The answer might be quick in coming. "There are lots of groups working in this area - it's a very competitive area."
The discovery that junk DNA helps cells regulate their own genes opens up a number of questions, he says. "We don't understand all the details of how the silencing is working. And the genes we've looked at are involved in sexual reproduction. Does this process control other genes?"
Andrew Read is a research scientist at the University of Edinburgh and a British Association for the Advancement of Science Media Fellow on placement at The Irish Times