ncDNA and drift drive binding site accumulation

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dc.citation.firstpage159en_US
dc.citation.journalTitleBMC Evolutionary Biologyen_US
dc.citation.volumeNumber12en_US
dc.contributor.authorRuths, Troyen_US
dc.contributor.authorNakhleh, Luayen_US
dc.date.accessioned2013-07-10T20:46:07Zen_US
dc.date.available2013-07-10T20:46:07Zen_US
dc.date.issued2012en_US
dc.description.abstractBackground: The amount of transcription factor binding sites (TFBS) in an organism's genome positively correlates with the complexity of the regulatory network of the organism. However, the manner by which TFBS arise and accumulate in genomes and the effects of regulatory network complexity on the organism's fitness are far from being known. The availability of TFBS data from many organisms provides an opportunity to explore these issues, particularly from an evolutionary perspective. Results: We analyzed TFBS data from five model organisms -- E. coli K12, S. cerevisiae, C. elegans, D. melanogaster, A. thaliana -- and found a positive correlation between the amount of non-coding DNA (ncDNA) in the organismﾒs genome and regulatory complexity. Based on this finding, we hypothesize that the amount of ncDNA, combined with the population size, can explain the patterns of regulatory complexity across organisms. To test this hypothesis, we devised a genome-based regulatory pathway model and subjected it to the forces of evolution through population genetic simulations. The results support our hypothesis, showing neutral evolutionary forces alone can explain TFBS patterns, and that selection on the regulatory network function does not alter this finding. Conclusions: The cis-regulome is not a clean functional network crafted by adaptive forces alone, but instead a data source filled with the noise of non-adaptive forces. From a regulatory perspective, this evolutionary noise manifests as complexity on both the binding site and pathway level, which has significant implications on many directions in microbiology, genetics, and synthetic biology.en_US
dc.embargo.termsnoneen_US
dc.identifier.citationRuths, Troy and Nakhleh, Luay. "ncDNA and drift drive binding site accumulation." <i>BMC Evolutionary Biology,</i> 12, (2012) BioMed Central: 159. http://dx.doi.org/10.1186/1471-2148-12-159.en_US
dc.identifier.doihttp://dx.doi.org/10.1186/1471-2148-12-159en_US
dc.identifier.urihttps://hdl.handle.net/1911/71524en_US
dc.language.isoengen_US
dc.publisherBioMed Centralen_US
dc.rightsThis article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/2.0/en_US
dc.titlencDNA and drift drive binding site accumulationen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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