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Junk genes - more than they're made out to be -

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Junk genes - more than they're made out to be

Genes to which geneticists have been able to ascribe a function have been described as junk genes.
And it's most of them. 90% or more. But are they? New research reveals the junk may be involved in
timing and control of gene expression, like a regulatory network. The human genome is 3 billion
bases. New machines will be able to output the equivalent of 30 human genomes in one experiment.
This will likely expose a whole new area of genetic information.


Robyn Williams: Now let me introduce you to another geneticist, this time in Brisbane where he's
studying junk. Yes, junk, as it's been called. Ryan Taft is a graduate student come to join one of
our resident world leaders in the field, Professor John Mattock at UQ.

Ryan Taft: Actually he's the whole reason I came here. We collaborated together when I was still
living in California, and we were looking at how much junk various genomes have. We saw this
correlation where vertebrates and other really complex organisms had a whole bunch of junk, and
this fit really well with all of his ideas about the non-junk stuff being really important.

Robyn Williams: The non-junk stuff is something like 93%, 94%, 95% of your DNA, and so it would be
astounding if all that stuff is there doing nothing in particular, and of course various people say
it's to do with the timing of various genes. For example, up to the age of 12 I did not need my
testosterone boost quite as much as I did when I suddenly turned the adolescent corner. Timing is
what it's all about. So is that the kind of thing mainly that the so-called junk DNA is supposed to
be used for?

Ryan Taft: Sure, timing and different tissue specificity, environmental cues, all that kind of
stuff. So we're really interested in teasing out what we think is a regulatory network that
overlays all of the genes that hides in the junk/non-junk.

Robyn Williams: You said tissues...for example, if my liver wants to do things that are programmed
in the DNA, it doesn't want to be distracted by DNA for a big toe or a left nipple, it wants to do
liver things. So is the junk saying 'concentrate on what you're good at, be a liver'? In other
words, that kind of specificity is what it's all about.

Ryan Taft: Yes, we think so, that's exactly right. The other thing we have to take into account
here is that the number of genes we have as humans and the number of genes a fruit fly has are
almost exactly the same. And not only that, the raw amount of sequence that's devoted to making
regular genes is almost the same, it's about ten million nucleotides. So something had to change to
make us humans, and fruit flies fruit flies. So we think that resides in the junk.

Robyn Williams: So what specifically are you actually doing in research now?

Ryan Taft: We're working with some really fascinating technologies, they're called deep sequencing
technologies or high throughput sequencing technologies. And when the human genome was sequenced it
took billions and billions of dollars and millions of machines and thousands and thousands of
people to put it all together. The human genome is about three billion bases. So we have machines
right now that they expect by the end of the year will be able to output 100 gigabases or 30
equivalents of the human genome in a single experiment.

So we've been using these experiments to really dig into this stuff in a way that nobody thought
was even possible five years ago. So we're looking for small RNAs, so these are components of the
regulatory system that are really, really tiny. So the most popular or well known form of these are
called micro RNAs and they're about 20 nucleotides long. Most average genes are 2,000, so these are
a lot smaller. We've been looking at micro RNAs and that's how we started to discover new small
RNAs that we think are part of the regulatory network.

Robyn Williams: When you refer to these RNAs, are they the ones that are the message that comes off
the DNA, the template? In other words, if the DNA is the code, the RNA is the message saying 'go
off and do that' which travels somewhere else to carry the instruction.

Ryan Taft: Exactly. So DNA is like the storehouse for all this information and RNA is the
intermediary, and then proteins are your final output, or at least that's the central dogma. So
what we're finding though is RNA does a whole lot of stuff on its own, and like we talked about
just a few minutes ago, genes are only about 2%. But we're finding that 90% of the human genome is
made into RNA. So the question is what is all that RNA doing, and we think it's helping to define
this liver tissue versus the big toe and all that stuff, yes.

Robyn Williams: What's the payoff, having crunched all these RNAs and looked at all the junk that
suddenly is not junk, when you surface from all this toil, how will we know the world has changed
to our benefit?

Ryan Taft: I think I can use one of the things we're working on right now as an example. So what
we've found is that RNA is even smaller than anyone expected; they are only 18 nucleotides long,
which when you consider the human genome as three billion, we're talking very, very tiny. And these
reside at the beginnings of genes, or kind of hiding in the very beginnings of genes. We have some
very tantalising evidence that these might be regulating how genes are turned on and turned off. So
one of the things we're speculating right now is that we might be able to use these to help turn on
and turn off genes exogenously, we might be able to introduce these into cells or take them out of
cells and start to work on therapeutic techniques using them. So I think there's going to be a lot
of little steps like this, I think it's always a gradual process in science, but little discoveries
like this tells us we're on the right track.

Robyn Williams: Ryan Taft is at the University of Queensland, a graduate student from California.
Catch them young and give them a boost. And of course money helps.