Is junk DNA bunk? A critique of encode

Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 4R2.
Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 03/2013; 110(14). DOI: 10.1073/pnas.1221376110
Source: PubMed

ABSTRACT Do data from the Encyclopedia Of DNA Elements (ENCODE) project render the notion of junk DNA obsolete? Here, I review older arguments for junk grounded in the C-value paradox and propose a thought experiment to challenge ENCODE's ontology. Specifically, what would we expect for the number of functional elements (as ENCODE defines them) in genomes much larger than our own genome? If the number were to stay more or less constant, it would seem sensible to consider the rest of the DNA of larger genomes to be junk or, at least, assign it a different sort of role (structural rather than informational). If, however, the number of functional elements were to rise significantly with C-value then, (i) organisms with genomes larger than our genome are more complex phenotypically than we are, (ii) ENCODE's definition of functional element identifies many sites that would not be considered functional or phenotype-determining by standard uses in biology, or (iii) the same phenotypic functions are often determined in a more diffuse fashion in larger-genomed organisms. Good cases can be made for propositions ii and iii. A larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon, is needed.

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    • "The recent publication of the numbers and distributions of epigenetic molecular signatures of noncoding DNA function in the human genome, the ENCODE paper (ENCODE Project Consortium, 2012), rekindled discussions on the general topic of ''junk DNA'' function, the correctness of logic as applied to molecular data, and on a long-standing related topic, the C-value paradox (Doolittle, 2013; Graur et al., 2013). We hope to solve the C-value paradox by supporting a bulk function for junk DNA. "
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    • "However, such studies are indicative only of biochemical activity, i.e. biochemical changes at the molecular level. These molecular processes do not always have an impact on organismal phenotypes or fitness (Eddy 2012; Niu and Jiang 2013; Doolittle 2013; de Souza et al. 2013). In other words, biochemical activity does not necessarily imply biological function. "
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    • "An element may have a function in the genome regardless of the level of selection that produced or maintains it. Doolittle is right in insisting on this point (Doolittle, 2013 "
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