We were doing experiments with transgenic plants, in which we were trying to make the plants resistant against virus infection. So we were taking genes out of a virus and expressing them as transgenes in a plant. For various reasons, we thought that would confer virus resistance. In fact some of them did, and we were very pleased about that.

“If you want to know what a gene does, the best thing to do is silence it and look at the effect on the organism.”

But—and this surprised us—plants that had the transgene that were resistant had the transgene switched off—it was silent. We had plants with the same transgene that were not resistant, and in those plants the transgene was not silent. We finally figured that the silencing mechanism that was shutting down the transgene in the plant was also conferring the resistance against the viruses.

The first paper we published on that was in 1993.

We wanted to know what was conferring the specificity. The resistance and the silencing mechanisms were nucleotide sequence-specific and we thought that it was probably working through antisense RNA.

Andrew Hamilton, my coauthor, who was a post-doc at the time, did lots of experiments looking for antisense RNA in any plants that were silencing genes. We extended our analysis away from plants that were just doing the silencing of viral transgenes, and Andrew started looking at a whole bunch of other plants as well. He tried for a long time. The success of the work was a real testimony to Andrew’s persistence. He tried looking for antisense RNAs and he couldn’t find them. Finally, we suspected that we might be running them off the end of the gel. Small RNA runs quickly. He adapted the methodology and started looking for short antisense RNA, and that indeed is when he found it.

He was probably working on it for about three years altogether.

This all panned out subsequently because it turned out that we were looking at the same mechanism that Craig Mello and Andrew Fire were looking for, and for which they just got the Nobel Prize. We were looking at the mechanism in plants; a lot of other people were looking at it in animals. It turns out it’s a universal mechanism. These little short RNAs are ubiquitous in RNA silencing, and that’s why it’s so significant.

That’s one of the open questions at the moment. In many respects the mechanisms are the same—but there may also be differences. In plants for example—as in fission yeast—the short RNAs direct epigenetic modifications to chromatin and DNA. The jury is still out as to whether or not animals have retained the potential to use these short RNAs for these same epigenetic mechanisms.

It’s gone in three main directions: One is towards a technology for shutting off genes. If you want to know what a gene does, the best thing to do is silence it and look at the effect on the organism. You can develop various ways of making these little short RNAs and using them to silence genes in both plants and animals. It’s a very useful experimental technology.

Another way a lot of people would like it to go is to use these short RNAs as an RNA drug. If you could find a way of delivering these RNA to animals so that you could silence a disease gene or a virus gene, you could develop therapeutics against that virus or that disease. You can also use strategies based on short RNA for improvement of crop plants.

The third direction the whole field is going is trying to look at endogenous short RNAs made in cells, irrespective of any transgenes, and asking what they do. There’s a whole family of endogenous silencing mechanisms and they are important in both genetic and epigenetic mechanisms.

That’s what we’re looking at now. I use a metaphor, originally used by Gary Ruvkin, who referred to these short RNAs as the dark matter of genetics. Just like dark matter in cosmology, there are an awful lot of these short RNAs in cells and they’re undoubtedly important in the behavior of the genetic or epigenetic universe. And up until a few years ago we didn’t even know they were there.

The challenge, in terms of my own research, is trying to fit these short RNAs into the big picture of biology. What do they do and what happens to the organism if it doesn’t make them? They’re not simple switches like transcription factors. It’s more complicated than that. So the big challenge for us is coming to grips with what they’re doing in terms of the biology of the organism.

We knew it was pretty important. So we knew we’d done something good when we found this out.

When we started working this field, it was like walking on an empty beach littered with gem stones. The beach was deserted, and wherever you’d walk, there was something valuable to pick up. Now a whole bunch of people have been over the beach. But there’s still stuff to find. It’s more of a challenge now, but that’s good. I like to work in an area that’s important with many people interested in the same topic. It’s a lot better than following up something unimportant and have nobody else interested.

I think that our understanding of these short RNAs will be integrated into a systems biology understanding of cells. I’m expecting that they influence robustness for complex regulatory systems. We have to start thinking at a systems level in order to understand where they fit.

One message you can take from our experience and others in this whole RNA interference, silencing field is that plants are just wonderful experimental systems. They’re just as good as yeast and as good as worms at revealing aspects of fundamental biology.

David Baulcombe, FRS
The Sainsbury Laboratory
John Innes Centre
Norwich, UK