ENCODE: The Encyclopedia of DNA Elements
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ENCODE: The Encyclopedia of DNA Elements


Mike Pazin:
As difficult as it was to find all of the information of the
genome, to sequence the genome, this next step of figuring out
what all the information is in the genome is a much more
complex problem. We’re just beginning to understand how
this works. Ross Hardison:
Our genome is very, very large and we’re trying to figure where
the parts of it make a difference in our lives, in our
susceptibility to disease, and maybe even impact our behaviors
in some ways. Elise Feingold:
The fundamental question we’re trying to answer is what does
all the genome do.? What are all the different functional
elements.? Rick Myers:
The whole purpose of the ENCODE project is to try to figure out
which base pairs in the human genome are important. And
that’s a big question because there are a lot of base pairs,
and the important ones are not all in one little package,
they are spread throughout. Ewan Birney:
And the human genome when it was finished, were the letters,
okay. What ENCODE is saying is, “Aha, I think this is a word, and
this is a word, and this is a word and this is a word. Ross Hardison:
If we could understand that, then we could start to figure
out who’s really likely to come down with type 2 diabetes, who’s
likely to get lung cancer, who should be making changes in
their lifestyles to try to prevent this, who’s going
to be most responsive to certain drugs. Mike Pazin:
There’s on the order of 5 percent of the genome, one-twentieth,
that you can ascribe function to. But that still leaves a large fraction
of the genome, maybe 95 percent, that embarrassingly we don’t
know what it does. And what ENCODE is able to do,
attribute function to a larger fraction of the genome than we
were able to see before. Rick Myers:
A big part of the project is to try to figure out where all the
proteins that interact with DNA — where they’re bound in a
particular cell at a particular time during a particular
process. You basically freeze the proteins onto the place in
the DNA in the nucleus while the cell’s still alive and then
analyze it afterwards. Ross Hardison:
You can get antibodies against those proteins and we can purify
out that subset of the genome that has a special property. We
get those molecules, we put them into the sequencers. Map them
back to the genome and figure out where these particular
chemical processes are happening. This is just amazing. Elise Feingold:
So it really gets you just a blueprint, where are you landing
and what genes are nearby. what tissues might that be active
in, so really it’s a starting point. Mike Pazin:
Very little of our genomes are junk. 80 percent of the genome is engaged
in at least one biochemical activity. For a large fraction of the genome,
not now 5 percent, but 80 percent of the genome, we can say that we
know that it does something. Ewin Birney:
This metaphor about junk DNA, it’s become, very entrenched.
It’s been entrenched publicly and entrenched scientifically.
And ENCODE totally challenges that. We just don’t have big,
blank, boring bits of the genome. All the genome is
alive at some level. Peter Good:
What ENCODE does is it provides a general catalogue of how the
genome functions, and so what they can do is, is they can take
their disease tissue — in the case of a diabetes researcher,
it would be a pancreas or a muscle cell in a diabetes
patient — and they can ask what genes are expressed, and then
they can look to see how genes are misregulated in these
tissues, and then they can start back to our catalogue and say,
okay, what are the elements, ENCODE elements, in front of
these genes? Ewan Birney:
We can take a disease like Crohn’s disease, which is a
pretty bad disease of the gut, and say to the people
studying it, “Well, have you thought about this particular
mechanism? Or this?” And sometimes they have; sometimes
it’s a bit of surprise. And they say, oh I am very interested in that. let
me go of and have a look. But we do that comprehensively
for hundreds of diseases compare alongside hundreds of different
mechanisms, and that’s been quite exciting. Ewan Birney:
Well there’s 2,000 binding proteins in the genome. We
looked at about 100 of those, 116 of those. So there’s a long
way to go yet. So there’s a lot more of these guys to study. Mike Pazin:
By having that larger store of information, I think that will
accelerate the pace of health care. The better we understand
it, the more of a chance that we could intervene in the system
in a beneficial way.

7 thoughts on “ENCODE: The Encyclopedia of DNA Elements

  1. Your right. We are still holding up the rotting corpse of Darwins outdated and obsolete theory. It is reminiscent of the movie a Weekend At Bernie's. The only difference is, that instead of music animating the corpse, its a courts gavel.

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