Is junk DNA bunk? A critique of ENCODE.
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. "
ABSTRACT: The Genome Balance Hypothesis originated from a recent study that provided a mechanism for the phenomenon of genome dominance in ancient polyploids: unique 24nt RNA coverage near genes is greater in genes on the recessive subgenome irrespective of differences in gene expression. 24nt RNAs target transposons. Transposon position effects are now hypothesized to balance the expression of networked genes and provide spring-like tension between pericentromeric heterochromatin and microtubules. The balance (coordination) of gene expression and centromere movement are under selection. Our hypothesis states that this balance can be maintained by many or few transposons about equally well. We explain known, balanced distributions of junk DNA within genomes, and between subgenomes in allopolyploids (and our hypothesis passes "the onion test" for any so-called solution to the C-value paradox). Importantly, when the allotetraploid maize chromosomes delete redundant genes, their nearby transposons are also lost; this result is explained if transposons near genes function. The Genome Balance Hypothesis is hypothetical because the position effect mechanisms implicated are not proved to apply to all junk DNA, and the continuous nature of the centromeric and gene position effects have not yet been studied as a single phenomenon. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.Molecular Plant 03/2015; 8(6). DOI:10.1016/j.molp.2015.02.009 · 6.61 Impact Factor
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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. "
ABSTRACT: Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions, and confirmed their robust functional signatures. 99.7% of ASC basepairs were noncoding, suggesting that novel anthropoid functional elements were overwhelmingly cis-regulatory. ASCs were highly enriched in loci associated with fetal brain development, motor coordination, neurotransmission and vision, thus providing a large set of candidate elements for exploring the molecular basis of hallmark primate traits. We validated ASC192 as a primate-specific enhancer in proliferative zones of the developing brain. Unexpectedly, transposable elements (TEs) contributed to >56% of ASCs, and almost all TE families showed functional potential similar to that of non-repetitive DNA. Three L1PA repeat-derived ASCs displayed coherent eye-enhancer function, thus demonstrating that the 'gene-battery' model of TE functionalization applies to enhancers in vivo. Our study provides fundamental insights into genome evolution and the origins of anthropoid phenotypes, and supports an elegantly simple new null model of TE exaptation.Genome Research 07/2014; Genome Res. 2014 Jul 20. pii: gr.168963.113.(pii: gr.168963.113.[Epub ahead of print]). DOI:10.1101/gr.168963.113 · 13.85 Impact Factor
- "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 "
Article: The genome as a developmental organ[Show abstract] [Hide abstract]
ABSTRACT: This paper applies the conceptual toolkit of Evolutionary Developmental Biology (evo-devo) to the evolution of the genome and the role of the genome in organism development. This challenges both the Modern Evolutionary Synthesis, the dominant view in evolutionary theory for much of the 20th century, and the typically unreflective analysis of heredity by evo-devo. First, the history of the marginalization of applying system-thinking to the genome is described. Next, the suggested framework is presented. Finally, its application to the evolution of genome modularity, the evolution of induced mutations, the junk DNA versus ENCODE debate, the role of drift in genome evolution, and the relationship between genome dynamics and symbiosis with microorganisms are briefly discussed.The Journal of Physiology 06/2014; 592(11). DOI:10.1113/jphysiol.2014.271734 · 4.54 Impact Factor