Human genome is over 90% ‘junk’ DNA – study

This undated handout illustration shows the DNA double helix (AFP Photo)
Less than 9.5 percent of human DNA is functional, according to Oxford University researchers. This overturns the mainstream theory that 80 percent of the human genome is of some biological importance.

The study published in the journal PLOS Genetics reveals that at present, a total of 8.2 percent (7.1 – 9.2 percent) of the human genome is functional – “more than three times as much than is functional and shared between human and mouse.” And even within that small percentage, some DNA can be found that performs more significant tasks.

A reproduction is pictured at the chamber of evolution of the Museum of Human Evolution (AFP Photo / Cesar Manso)This evaluation contradicts another figure given back in 2012, when participants of the ENCODE (Encyclopedia of DNA Elements) project estimated that 80 percent of the human genome has some biochemical function.

But the biochemical definition of “function” was criticized as too broad. Just because a DNA activity occurs does not mean it has a consequence; the activity itself should have importance. The difference between the approaches raises a profound question which still remains unanswered, over a decade after the finishing of the human reference genome sequence. That is, what fraction of the human genome has actual function, if 99 percent of it does not encode proteins?

“We tend to have the expectation that all of our DNA must be doing something. In reality, only a small part of it is,”said Dr. Chris Rands, first author of the study and a former Doctor of Philosophy student in the MRC Functional Genomics Unit at Oxford University.

The cornerstone of the new definition proposed in the study is the ability of evolution to separate the sheep from the goats – in other words, to unearth which activities matter and which do not.

“This is in large part a matter of different definitions of what is ‘functional’ DNA,” said joint senior author Professor Chris Pointing of the MRC Functional Genomics Unit at Oxford University. “We don't think our figure is actually too different from what you would get looking at ENCODE's bank of data using the same definition for functional DNA.”

The researchers studied the changes in DNA in over 100 million years of mammalian evolution. Dr. Gerton Lunter from the Wellcome Trust Centre for Human Genetics at Oxford University, the other joint senior author of the study, explained: “Throughout the evolution of these species from their common ancestors, mutations arise in the DNA and natural selection counteracts these changes to keep useful DNA sequences intact.”

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Using a computational approach, the scientists compared the complete DNA sequences of various mammals – from mice, guinea pigs, and rabbits to duckbills, horses, and humans – to find where chunks of DNA were inserted or deleted. Though it is possible for this to happen randomly, cases were also found when natural selection played its part.

“We found that 8.2 percent of our human genome is functional,” said Dr. Lunter. “We cannot tell where every bit of the 8.2 percent of functional DNA is in our genomes, but our approach is largely free from assumptions or hypotheses. For example, it is not dependent on what we know about the genome or what particular experiments are used to identify biological function.”

So, what kind of biological baggage is left to us? The rest of our genome – over 90 percent – turns out to be leftover evolutionary material, which is often called “junk” DNA. But is it garbage?

"We haven't been designed. We've evolved and that's a messy process. This other DNA really is just filler. It's not garbage. It might come in useful one day. But it's not a burden," Dr. Lunter told the Guardian.