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ncDNA and drift drive binding site accumulation
BACKGROUND: 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 o...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556125/ https://www.ncbi.nlm.nih.gov/pubmed/22935101 http://dx.doi.org/10.1186/1471-2148-12-159 |
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author | Ruths, Troy Nakhleh, Luay |
author_facet | Ruths, Troy Nakhleh, Luay |
author_sort | Ruths, Troy |
collection | PubMed |
description | BACKGROUND: 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’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. |
format | Online Article Text |
id | pubmed-3556125 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35561252013-01-31 ncDNA and drift drive binding site accumulation Ruths, Troy Nakhleh, Luay BMC Evol Biol Research Article BACKGROUND: 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’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. BioMed Central 2012-08-30 /pmc/articles/PMC3556125/ /pubmed/22935101 http://dx.doi.org/10.1186/1471-2148-12-159 Text en Copyright ©2012 Ruths and Nakhleh; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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. |
spellingShingle | Research Article Ruths, Troy Nakhleh, Luay ncDNA and drift drive binding site accumulation |
title | ncDNA and drift drive binding site accumulation |
title_full | ncDNA and drift drive binding site accumulation |
title_fullStr | ncDNA and drift drive binding site accumulation |
title_full_unstemmed | ncDNA and drift drive binding site accumulation |
title_short | ncDNA and drift drive binding site accumulation |
title_sort | ncdna and drift drive binding site accumulation |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556125/ https://www.ncbi.nlm.nih.gov/pubmed/22935101 http://dx.doi.org/10.1186/1471-2148-12-159 |
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