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ENCODE Explosion

The Encyclopedia of DNA Elements, or ENCODE, project just published a glut of papers —30 publications in a variety of journals from more than 440 researchers — looking at the function of various regions of the human genome. The project's "aim is to catalogue the 'functional' DNA sequences that lurk there, learn when and in which cells they are active and trace their effects on how the genome is packaged, regulated and read," writes Brendan Maher at Nature. Nature has set up special portal housing the ENCODE papers and commentary.

In the overview paper in Nature, the ENCODE researchers note that 80 percent of the human genome has a biochemical function. Further, in The New York Times, Gina Kolata writes that researchers found that "the human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as 'junk' but that turn out to play critical roles in controlling how cells, organs and other tissues behave."

ENCODE researcher Ewan Birney tells Ed Yong at Not Exactly Rocket Science that that 80 percent figure will increase, possibly reach as high as 100 percent. "We don't really have any large chunks of redundant DNA," Birney says. "This metaphor of junk isn't that useful." (Birney has his own blog post here.)

In the Times Eric Lander likens the work to Google Maps. The Human Genome Project "was like getting a picture of Earth from space," he says. "It doesn't tell you where the roads are, it doesn't tell you what traffic is like at what time of the day, it doesn't tell you where the good restaurants are, or the hospitals or the cities or the rivers."

At his blog, Michael Eisen says that how much of the ENCODE work has been presented, both in press releases and in news accounts, is incorrect — he calls part of Kolata's characterization of the work (quoted above) "complete crap," but says it was nearly inevitable given how the project has been portrayed. He adds that Birney, in his own blog post gave a measured account of the 80% idea. There, Birney says "a conservative estimate of our expected coverage of exons + specific DNA:protein contacts gives us 18%, easily further justified (given our sampling) to 20%." But Eisen says that "his quotes in the press release play a bit fast and loose with this issue."

Others like T. Ryan Gregory at Genomicron and Leonid Kruglyak on his Twitter feed also take issue with the 80 percent figure. Gregory notes that the figure is for sequences with biological activity, which he says is "a term even more loosely defined than 'function.'" He adds that the researchers chose that number as " a) it generates attention, and b) people are too busy to grasp a nuanced discussion of '20% potentially functional given present evidence, but up to 80% has some kind of activity that might also imply function.'"

Daily Scan's sister publication GenomeWeb Daily News has more on the ENCODE papers here.