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.
"all experimentally defined regulatory elements are expected to be functionally or phenotypically significant (Eddy 2012; Doolittle 2013; Graur et al. 2013; Niu and Jiang 2013). Thus, we hypothesized that the synergistic combination of comparative and functional genomics would facilitate the highresolution identification of conserved and human accelerated regulatory sequences. "
[Show abstract][Hide abstract] ABSTRACT: It has long been hypothesized that changes in gene regulation have played an important role in human evolution, but regulatory DNA has been much more difficult to study compared with protein-coding regions. Recent large-scale studies have created genome-scale catalogs of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To better define regulatory DNA that has been subject to human-specific adaptive evolution, we performed comprehensive evolutionary and population genetics analyses on over 18 million DHSs discovered in 130 cell types. We identified 524 DHSs that are conserved in nonhuman primates but accelerated in the human lineage (haDHS), and estimate that 70% of substitutions in haDHSs are attributable to positive selection. Through extensive computational and experimental analyses, we demonstrate that haDHSs are often active in brain or neuronal cell types; play an important role in regulating the expression of developmentally important genes, including many transcription factors such as SOX6, POU3F2, and HOX genes; and identify
striking examples of adaptive regulatory evolution that may have contributed to human-specific phenotypes. More generally, our results reveal new insights into conserved and adaptive regulatory DNA in humans and refine the set of genomic substrates that distinguish humans from their closest living primate relatives.
"In thus extending the upper bounds of an undifferentiated " functionality " into territory occupied by TEs without acknowledging that there are other (genome level) selective processes at play to explain the presence of so much DNA, ENCODE investigators dismiss much previous theory in genome evolution (Doolittle 2013; Palazzo and Gregory 2014; Elliott et al. 2014). Some ENCODE supporters even claim to have at last exposed ignorant and possibly willful bias on the part of evolutionary theorists who have argued for junk and selfish DNA. "
"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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