Different views on the proportion of the genome that is encoding

This week we will discuss two papers on the proportion of the genome that is encoding, "An integrated encyclopedia of DNA elements in the human genome" authored by The Encode Project Consortium published in Nature 2012, and a critique entitled "On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE" by Graur and colleagues published in GBE 2013.

Abstracts:

An integrated encyclopedia of DNA elements in the human genome (The Encode Project Consortium, Nature, 2012):

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

On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE (Graur et al., GBE 2013):

A recent slew of ENCyclopediaOfDNAElements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according towhich the fraction of the genome that is evolutionarily conserved through purifying selection is less than10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80-10=70% of the genome is perfectly invulnerable to deleteriousmutations, either because no mutation can ever occur in these “functional” regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as“affirming the consequent,” by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivityover specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.
Published Jan. 6, 2014 3:19 PM - Last modified Jan. 7, 2014 10:34 AM