Did a gene enhancer humanise our thumbs?

By Ed Yong | September 4, 2008 2:00 pm

Blogging on Peer-Reviewed ResearchThe image on the right is both beautiful and exciting. Let me explain why. It’s the paw of an embryonic mouse and a team of geneticists have inserted a fragment of human DNA into its cells. The fragment contains an “enhancer” element, a short span of DNA that switches other genes on and off; in this case, they put the enhancer in control of a gene whose activity creates a blue chemical.

Thumb.jpgThis particular enhancer is called HACNS1. Throughout the course of animal evolution, its sequence has gone relatively unchanged in almost all back-boned animals, but it has evolved rapidly in the human genome since we split away from chimpanzees. So the blue patch in this image shows where this rapidly-evolved, human-specific piece of DNA is triggering genetic activity in the paw of a mouse. Figured out why it’s exciting yet?  It’s in the bit that will eventually become a thumb.

Evolving enhancers

HACNS1 controls genes but it isn’t one itself. It is part of the large majority of our genome known as “non-coding DNA“. A small proportion of our DNA is a code that tells our cells how to build its workforce of proteins, but the majority is never translated in this way. Much of this “non-coding DNA” is functionless junk, but some types are very important indeed.

The enhancers are one such group. They are stretches of DNA that control the activity of genes, which can often lie some distance away from the enhancer. When “activator” proteins stick to the enhancers, the target gene is switched on.

Change the sequence of these enhancers and you can change which genes they control, when they do so and where they do so. It’s one way for evolution to exact big changes in a creature’s body without having to add much in the way of genetic innovation. By changing enhancers, it can simply redeploy the existing squad of genes in new and interesting ways. The results can be dramatic, much like changing a sports manager can have a greater impact on a team’s performance than switching out individual players.

There’s evidence that these sorts of changes have indeed happened. Many human non-coding sequences show signs of incredibly rapid evolution ever since our evolutionary path diverged from that of chimps some six million years ago. Shyam Prabhakar from the Lawrence Berkeley National Laboratory singled out HACNS1 for attention because it is the most rapidly evolving sequence of its kind.

Only 16 differences separate HACNS1’s sequence from that of its chimp counterpart, but that’s about 4 times as many as you would have expected if the sequence had just been drifting aimlessly while picking up new mutations. These rapid changes are a clear sign of “positive selection”, where new mutations  bestow such advantages on their bearers that they spread rapidly throughout the population.

All thumbs

So what does HACNS1 do? To find out, Prabhakar (together with a large team of geneticists) placed the human, chimp and macaque versions in a strain of mice. They set things up so that the sequence had control over a gene that creates a blue chemical when it’s active. At the time, no one knew if HACNS1 was an enhancer; that only became apparent when they saw patches of blue in the young mouse embryos.

HACNS1.jpgEmbryos that were loaded with the human version had strong blue stains in their developing limbs, eyes, ears and pharyngeal arches (structures that will eventually become the muscles, bones and organs of the mouth and throat). As the embryo develops, HACNS1 is clearly acting as a gene enhancer in these body parts. In comparison, the chimp and macaque versions drove very little gene activity at these sites, particularly at the limbs, where many embryos had no signs of blue colour at all.

When the team looked at older embryos, they saw that the enhancer was still activating genes in the young mouse’s limbs. They saw the telltale blue stain in the shoulder, wrist and thumb of the front limbs and to a lesser extent in the big toe, ankle and hip of the hind pair. Once again, the chimp and macaque enhancers were far less enhancing, and only drove a smattering of gene activity in the shoulder area.

The results are preliminary but they are exciting. They suggest that changes in HACNS1 may have contributed to the uniquely human aspects of our thumbs, wrists, ankles and feet.  Our long and fully opposable thumbs allow us to grip and manipulate objects with great precision while our inflexible feet and short toes give us the stability that life on two feet demands. There’s no doubt that these physical innovations have played a key part in our success as a species, and perhaps HACNS1 can take some credit for that.

Sweet sixteen

Prabhakar’s team found further proof of the uniqueness of human HACNS1 with a deceptively simple game of genetic swapsies. They added all 16 human-specific changes to the chimpanzee version, and also stripped out all 16 changes from the human sequence to revert it back to the chimp one. In the mouse embryos, the “humanised” chimp enhancer produced the same pattern of blue as the natural human version did (compare top right embyros with bottom left), while the “reverted” human enhancer yielded the same pattern as the untouched chimp and macaque ones (compare bottom right with top left).


These 16 genetic tweaks have raised HACNS1’s profile, turning it from a bit-part actor into one of the major stars in the drama of development. It’s not entirely clear how this has happened, but a quick analysis showed that the 16 changes have probably altered the way that the enhancer interacts with its activator proteins. The proteins attach to the enhancer through specific docking sites that are dictated by its sequence. As this sequence changed in 16 ways, docking sites were added for some proteins and lost for others.

The next part of the quest will be to find which genes are enhanced by the enhancer. The closest two are CENTG2, whose role in limb development has never been looked at, and GBX2, which is activated in embryonic limbs. Nor is the role of  HACNS1 confined to limbs – it’s also activated in eyes, ears and the precursors of mouths. And perhaps there are other organs that are affected in humans but don’t show up in the mouse embryos. These are all questions for another time. For now, the results can be taken as yet further evidence that many of evolution’s big breakthroughs, from eyes to language, are the result of genetic tinkering rather than novelty.

Reference: 10.1126/science.1159974

Images: from Science

CATEGORIZED UNDER: Evolution, Genetics, Human evolution

Comments (10)

  1. Matt

    Amazing! I liked this article alot! Imagine where this could go…

  2. I thought that chimps had thumbs on their feet too? I’ve always been a little jealous of that, especially when up in a tree (although mountain goats can climb mountains much better with only hooves).
    But regardless – hitchhiking mice don’t seem as interesting as sticking these genes into a chimp to see if we can get them to play basketball.

  3. Another of your great ones. Perhaps exploring of genes this way may throw light on genetics, embryology and immunology. They may also suggest that not all junk DNAs are that junk. Pharmaceutical industries might also try ‘a variant of this’ for the ‘blocking’ of switches in managing genetic diseases.

  4. Nice article, nice picture. Really good to read a text about this research that focus on the importance of the gene, not the “junk DNA” thing.
    About the mutations that differ human sequence from chimp sequences: there are 13 changes.

  5. No there aren’t – there are 16. I’ve just checked the paper. Thirteen of those happen to sit within a tight cluster, but there are three more outside of it.
    Re the “junk DNA” thing: the idea that scientists have until recently thought that non-coding DNA is all junk is a fabrication of journalists. If you look back historically, you find very old discussions about functional non-coding DNA. I’ve been chastised for making this error before – check out Genomicron for a lot more on this.

  6. Or in fact, read Carl Zimmer’s take over at the Loom, where he makes the same point as the above comment, only much better.

  7. Bee

    Very interesting article, Ed – thank you.
    Although the thought of mice with thumbs started off an awful earworm of the ‘Pinky and the Brain’ theme song…

  8. miko

    The first published of these human-accelerated regions, HAR1, a brain-expressed miRNA, got lots of press because it appears to be under rapid positive selection. There was some follow-up analysis pointing out that rapid change and fixation can occur through biased gene conversion, where the G or C allele of a SNP spreads rapidly due to a meiotic quirk I only vaguely understand. In other words, it’s possibly a genetic hiccup, not a functional adaptation.
    Anyway, the take home is that the appearance of rapid positive selection in sequence data can be deceiving. You need functional data. They start to get at it here, the problem is enhancer binding can be a very noisy, complicated process, and this paper doesn’t use real genes as a readout.
    Not knocking it, just saying its a few steps away from what they seem to want to conclude, or want the science media to conclude base on their press release. And the reasoning of this “conclusion” is suspect and very science journalistic: there is something different about our limbs, and there is something different about this enhancer, therefore (even assuming this enhancer is doing anything!) changes to this enhancer drove limb evolution?
    On a purely practical level, of course, it seems like in evo-devo the cis and trans regulatory camps are desperate for data to wave at each other, so this kind of paper is hot and you can publish really well!

  9. Thanks for this interesting article, Ed!

  10. megan

    Does it work in conjunction with the later human adapted FOXP2 gene for communication? And what of animals with very dexterous thumbs besides primates. Does this gene show any activity for them or different digits? I’m thinking of the many omnivore and rodents who sue their ‘paw’ thumbs very well like raccoons, otters and squirrels. FOXP2 in Parrots is shown to be very involved in their vocalizing use of tongue, in as much as it seems for human.


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