Are critics exaggerating ENCODE’s emphasis on function?

Here and there in the blogosphere, people have begun defending ENCODE against criticism by noting that there is a lot more to the project than just the claim that 80% of the genome is functional. That’s just the media, they say, whereas that was only a small part of the actual study.

Well, it’s certainly the one thing that the media seems to be reporting on, and it’s what the researchers have been talking about with the media. But what about the actual publication? Let me remind you that this is what the abstract of the main ENCODE paper states (emphasis added):

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

And here is the very first bullet point in the summary of the project’s key findings:

The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type. Much of the genome lies close to a regulatory event: 95% of the genome lies within 8 kilobases (kb) of a DNA–protein interaction (as assayed by bound ChIP-seq motifs or DNase I footprints), and 99% is within 1.7 kb of at least one of the biochemical events measured by ENCODE.

In this case, I don’t think the media are creating the hype all by themselves or missing the main message of the primary paper.

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