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Thursday, September 13, 2012

Introducing ENCODE

A huge international project called the ‘Encyclopedia of DNA Elements’ (ENCODE) is now ready for prime time. This week, some thirty papers have been published explaining what it is and what it might mean. For a far more comprehensive discussion than I can give here, you can’t go wrong with Ed Yong’s tour de force at Not Exactly Rocket Science.

In a nutshell, ENCODE is an enormous manual for the human genome. Now that we’ve sequenced all those stretches of Gs, Ts, As and Cs, what exactly are they doing? The ENCODE analyses are as interesting for what they disprove as they are for what they demonstrate.

For example, have you heard that over 95% of the human genome is ‘junk DNA’, not really of any use to us? Wrong! It turns out that nearly every part of our genomes might serve some function. That doesn’t mean the number of genes was grossly underestimated. We still think that only a few percent of our DNA codes for proteins. It’s just that lots of non-coding sections of DNA are used either to make regulatory RNAs, or simply as landing zones for RNAs and proteins. 

Another thing ENCODE tackles is the problem of how and why our myriad cell types differ from each other. You’re not going to get very far in figuring out why we aren’t chimps if you can’t even say why we aren’t just giant livers rather than being composed of more than a thousand distinct cell types.

For a summary from some of the lead researchers, see below:

And for a more visual explanation, leave it to Ian Sample of The Guardian:

Obviously, much more data is going to come out of this immense collaboration. In the meantime, you can look over the results yourself at the ENCODE website.


  1. The results are not quite so conclusive as Ed Jong first explained. The problem appears to rest around the ENCODE's definition of 'function'. Have a look at Larry Moran's site for a far better explanation than I can give.

  2. Good point. That's partly why I didn't include the 80% figure; I don't think that will stand. Obviously, our genomes do have a lot of nonfunctioning pseudogenes and defective transposons, as Moran and others have stated. However, ENCODE confirms that much of our noncoding DNA is definitely not useless.

    One reason I chose to link to Yong's post was because he includes updates and links to other commentary, including several from Moran.