How did nucleosomes evolve?

16 June 2013

Interview with

Corey Nislow, University of British Columbia

eLife LogoHow did our cells come by their nucleosomes?  These are short stretches of DNA wrapped around a sort of protein ball.  The nucleosomes help us to pack DNA tightly inside our cell nuclei.  They also control when genes get turned on and off. 

Corey Nislow at the University of British Columbia has discovered that these structures were probably doing something else before they were turned by our sorts of cells into spools for DNA. He explains this to Kat Arney.

Corey -   We noticed that nucleosomes occupied in very characteristic positions in the genome.  As any good biologist would do, we set about trying to perturb that, and we spent a lot of time looking at mutants in yeast and some of these mutants in yeast were extremely informative, but most weren't.  And so, we went to look at an extreme environment - to push the system to failure to the point where we knew we were going to see some kind of - if we didn't see a dramatic change in the location of nucleosomes, we would really start to wonder what's going on.  So, we started to look for extremophilic organisms - organisms that live in near boiling water or near saturated solutions of salt.  As we were looking for eukaryotes in those environments, we kept finding archae-bacterial organisms.  They were all over the place - in boiling water environments, in environments where the salt concentration is so high that the salt were actually precipitating out of solution, like in the Dead Sea.  Rather than keep looking for eukaryotes in those environments, we started to say, "Well, maybe we should look at these Archaea." Archaea have nucleosomes that are remarkably similar to eukaryotic nucleosomes except they're half-size.  Using new mapping technology, specifically next-generation sequencing, we prepared nucleosomes from archaea and we also prepared RNA at the same time.  So, we can ask - one, is the organisation the same in archaea as it is in eukaryotes?  Two, is this correlation that we see between gene expression and nucleosome positioning maintained?  I wouldn't be talking to you if the answer to both questions wasn't yes!

Kat -   So, what did you find?

Corey -   So, we found that this parallel universe is exactly what's going on in that the entirety of the archaea bacterial genome is wrapped up in nucleosomes.  It's the frequency of the wraps, they are twice that of what you see in eukaryotes because they're half the size and they only wrap half as much DNA.  The regions that have fewer nucleosomes are regions at the beginnings and ends of genes where other proteins need to fight for access to the DNA to turn things on and off.

Kat -   And that's exactly what you find in eukaryotes as well.

Corey -   That's why I was saying it's really like a parallel universe for us.

Kat -   When you found this, what did you think because traditionally, there's been views that archaea and eukaryotes are very separate in terms of their evolution and they're separate branches of an evolutionary tree?  What do you think now in the light of your experiments?

Corey -   I really, really feast on the thought of as a wonderful device for packing DNA into a tiny space.  Each of us has over 4 meters of DNA, but we have to squeeze down into a nucleus that's only 5 millionth of a meter in diameter.  And so, one of the things they must be doing is serving as - we often use, 'packing material'.  But archaea don't have nuclei and therefore, don't have the same constraints of really shoving all of their DNA into such a tight space.  And so, we let ourselves wonder if given the fact that the nucleosomes in archaea are intimately linked with the gene expression patterns that maybe evolution first used nucleosomes to control gene expression.  And then shortly thereafter, when came a time to get everything into the nucleus, it co-opted that mechanism.  This wouldn't be the first case we're approaching this moonlight and served multiple functions.

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