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Network-dosage compensation topologies as recurrent network motifs in natural gene networks
BACKGROUND: Global noise in gene expression and chromosome duplication during cell-cycle progression cause inevitable fluctuations in the effective number of copies of gene networks in cells. These indirect and direct alterations of network copy numbers have the potential to change the output or act...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071340/ https://www.ncbi.nlm.nih.gov/pubmed/24929807 http://dx.doi.org/10.1186/1752-0509-8-69 |
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author | Song, Ruijie Liu, Ping Acar, Murat |
author_facet | Song, Ruijie Liu, Ping Acar, Murat |
author_sort | Song, Ruijie |
collection | PubMed |
description | BACKGROUND: Global noise in gene expression and chromosome duplication during cell-cycle progression cause inevitable fluctuations in the effective number of copies of gene networks in cells. These indirect and direct alterations of network copy numbers have the potential to change the output or activity of a gene network. For networks whose specific activity levels are crucial for optimally maintaining cellular functions, cells need to implement mechanisms to robustly compensate the effects of network dosage fluctuations. RESULTS: Here, we determine the necessary conditions for generalized N-component gene networks to be network-dosage compensated and show that the compensation mechanism can robustly operate over large ranges of gene expression levels. Furthermore, we show that the conditions that are necessary for network-dosage compensation are also sufficient. Finally, using genome-wide protein-DNA and protein-protein interaction data, we search the yeast genome for the abundance of specific dosage-compensation motifs and show that a substantial percentage of the natural networks identified contain at least one dosage-compensation motif. CONCLUSIONS: Our results strengthen the hypothesis that the special network topologies that are necessary for network-dosage compensation may be recurrent network motifs in eukaryotic genomes and therefore may be an important design principle in gene network assembly in cells. |
format | Online Article Text |
id | pubmed-4071340 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40713402014-06-27 Network-dosage compensation topologies as recurrent network motifs in natural gene networks Song, Ruijie Liu, Ping Acar, Murat BMC Syst Biol Research Article BACKGROUND: Global noise in gene expression and chromosome duplication during cell-cycle progression cause inevitable fluctuations in the effective number of copies of gene networks in cells. These indirect and direct alterations of network copy numbers have the potential to change the output or activity of a gene network. For networks whose specific activity levels are crucial for optimally maintaining cellular functions, cells need to implement mechanisms to robustly compensate the effects of network dosage fluctuations. RESULTS: Here, we determine the necessary conditions for generalized N-component gene networks to be network-dosage compensated and show that the compensation mechanism can robustly operate over large ranges of gene expression levels. Furthermore, we show that the conditions that are necessary for network-dosage compensation are also sufficient. Finally, using genome-wide protein-DNA and protein-protein interaction data, we search the yeast genome for the abundance of specific dosage-compensation motifs and show that a substantial percentage of the natural networks identified contain at least one dosage-compensation motif. CONCLUSIONS: Our results strengthen the hypothesis that the special network topologies that are necessary for network-dosage compensation may be recurrent network motifs in eukaryotic genomes and therefore may be an important design principle in gene network assembly in cells. BioMed Central 2014-06-14 /pmc/articles/PMC4071340/ /pubmed/24929807 http://dx.doi.org/10.1186/1752-0509-8-69 Text en Copyright © 2014 Song et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Song, Ruijie Liu, Ping Acar, Murat Network-dosage compensation topologies as recurrent network motifs in natural gene networks |
title | Network-dosage compensation topologies as recurrent network motifs in natural gene networks |
title_full | Network-dosage compensation topologies as recurrent network motifs in natural gene networks |
title_fullStr | Network-dosage compensation topologies as recurrent network motifs in natural gene networks |
title_full_unstemmed | Network-dosage compensation topologies as recurrent network motifs in natural gene networks |
title_short | Network-dosage compensation topologies as recurrent network motifs in natural gene networks |
title_sort | network-dosage compensation topologies as recurrent network motifs in natural gene networks |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071340/ https://www.ncbi.nlm.nih.gov/pubmed/24929807 http://dx.doi.org/10.1186/1752-0509-8-69 |
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