Hidden ‘junk’ gene separates human brains from chimpanzees

Scientists used to believe that 98.5% of our DNA is junk and serves no useful purpose. But new discoveries are showing that this assumption is wrong. We now know that one of the most important genes that separates humans from chimpanzees lies among this supposed junk.


We’ve all found gems hidden among junk before – the great album you own but never listened to, the book on your shelf that you never read, or the boot sale item that’s worth a fortune. Geneticists are no different. Last month, Katherine Pollard and Sofie Salama discovered that one of the most important genes in human evolution has been lying in plain sight, hidden within a pile of genetic junk.

Humans and chimps share over 98.5% of our DNA.

Humans and our closest cousins, chimpanzees, evolved from a common ancestor, and we famously share anywhere from 96-99% of our DNA. This similarity suggests an obvious question: what are the key genetic differences that separate us from chimps? The search for these differences is now possible because the entire human and chimp genomes have been sequenced. The genomes represent each species’ entire DNA repertoire and by comparing them, Pollard and Salama sought to hunt down the genetic innovations that shaped our very humanity.

The duo and their colleagues at the University of California, Santa Cruz, clocked the rate of evolution in different parts of the human genome. They specifically looked for bits that had remained relatively stable for eons, but had exploded into evolutionary action since we and chimps diverged form our common ancestor.

They found 47 such areas which they appropriately named ‘human accelerated regions’ or HARs. And among these, a clear winner emerged – HAR1, a stretch of DNA that had changed 18 times faster than expected since the human and chimp dynasties split. HAR1 is part of a gene called HAR1F, and when the duo homed in on its location, they were in for a shock.

Hidden gems

98.5% of our DNA is apparently junk

HAR1F is part of our so-called ‘junk DNA’. DNA is a code that becomes useful when it is deciphered into messages written in a related molecule called RNA. RNA messages then act as recipes for building the molecular workforce of our bodies, proteins. But 98.5% of our genes do not code for proteins.

This poorly-named ‘junk DNA’ produces RNA messages that are never translated. For a time, they were largely thought to be ignored by evolutionary forces, and while some research hinted at an active function, actual details about their roles have remained elusive.

Over the last decade or so, geneticists have come to appreciate that certain stretches of ‘junk DNA’ may actually be vitally important. The discovery of HAR1F provides massive evidence that this line of thought is correct. In fact, 47 out of the 49 HARs were found among junk DNA and many of these lie next to genes that code for proteins involved in brain development.

Pollard and Salama believe that HAR1F and its colleagues control when, where and how these brain development genes are switched on, effectively redeploying our protein arsenal in interesting ways. When they looked at the brains of embryos, they found that HAR1F showed up between the second and fifth months of development. It is found in special brain cells called Cajal-Retzius cells, which control the migration of neurons from their birthplace to other parts of the brain.

It is unsurprising that one of the fastest evolving genes in our collection affects the brain or that many of the other HARs also control brain development. After all, our large brains (three times larger than a chimp’s) are arguably our most defining attribute. But this study suggests that evolution fashioned our brains not by substituting in new proteins but by creatively changing the formation and tactics of the existing squad.

The evidence has never been stronger that the previously over-looked 98.5% of our genome is far from junk. Instead, this is an area littered with hidden gems that are essential to being human.

Reference: Pollard, Salama, Lambert, Lambot, Coppens, Pedersen, Katzman, King, Onodera, Siepel, Kern, Dehay, Igel, Ares, Vanderhaeghen & Haussler. 2006. Nature. Epub ahead of print.

Related posts on DNA and chimp/human evolution:
Non-coding DNA drove brain evolution by making nerve cells stickier
Chimps have more adaptive genetic changes than humans
Opinion: Not so unique – the chimpanzee Stone Age, and our place among intelligent animals
Chimps show that actions spoke louder than words in language evolution
Orang-utan study suggests that upright walking may have started in the trees



2 Responses

  1. nice article ed. i think the whole field of rna analysis is going to be the Next Big Thing…

    does HAR1 make a functional protein then? or is it just a ‘useless’ rna transcript? the nature link doesn’t work…


  2. Cheers Henry. No, HAR1F doesn’t produce any proteins – it makes an RNA transcript.

    However, based on the sequence, the authors worked out that it folds into a stable three-dimensional structure. This structure is much the same in various vertebrate groups but when we get to humans, it becomes radically different. Intriguing, no?


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