Stability depends on positive autoregulation in Boolean gene regulatory networks.
Network motifs have been identified as building blocks of regulatory networks, including gene regulatory networks (GRNs). The most basic motif, autoregulation, has been associated with bistability (when positive) and with homeostasis and robustness to noise (when negative), but its general importanc...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-11-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC4222607?pdf=render |
| _version_ | 1818133903585574912 |
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| author | Ricardo Pinho Victor Garcia Manuel Irimia Marcus W Feldman |
| author_facet | Ricardo Pinho Victor Garcia Manuel Irimia Marcus W Feldman |
| author_sort | Ricardo Pinho |
| collection | DOAJ |
| description | Network motifs have been identified as building blocks of regulatory networks, including gene regulatory networks (GRNs). The most basic motif, autoregulation, has been associated with bistability (when positive) and with homeostasis and robustness to noise (when negative), but its general importance in network behavior is poorly understood. Moreover, how specific autoregulatory motifs are selected during evolution and how this relates to robustness is largely unknown. Here, we used a class of GRN models, Boolean networks, to investigate the relationship between autoregulation and network stability and robustness under various conditions. We ran evolutionary simulation experiments for different models of selection, including mutation and recombination. Each generation simulated the development of a population of organisms modeled by GRNs. We found that stability and robustness positively correlate with autoregulation; in all investigated scenarios, stable networks had mostly positive autoregulation. Assuming biological networks correspond to stable networks, these results suggest that biological networks should often be dominated by positive autoregulatory loops. This seems to be the case for most studied eukaryotic transcription factor networks, including those in yeast, flies and mammals. |
| first_indexed | 2024-12-11T09:00:07Z |
| format | Article |
| id | doaj.art-9053354c99b3494b8c2e27888514c215 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-11T09:00:07Z |
| publishDate | 2014-11-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-9053354c99b3494b8c2e27888514c2152022-12-22T01:13:47ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582014-11-011011e100391610.1371/journal.pcbi.1003916Stability depends on positive autoregulation in Boolean gene regulatory networks.Ricardo PinhoVictor GarciaManuel IrimiaMarcus W FeldmanNetwork motifs have been identified as building blocks of regulatory networks, including gene regulatory networks (GRNs). The most basic motif, autoregulation, has been associated with bistability (when positive) and with homeostasis and robustness to noise (when negative), but its general importance in network behavior is poorly understood. Moreover, how specific autoregulatory motifs are selected during evolution and how this relates to robustness is largely unknown. Here, we used a class of GRN models, Boolean networks, to investigate the relationship between autoregulation and network stability and robustness under various conditions. We ran evolutionary simulation experiments for different models of selection, including mutation and recombination. Each generation simulated the development of a population of organisms modeled by GRNs. We found that stability and robustness positively correlate with autoregulation; in all investigated scenarios, stable networks had mostly positive autoregulation. Assuming biological networks correspond to stable networks, these results suggest that biological networks should often be dominated by positive autoregulatory loops. This seems to be the case for most studied eukaryotic transcription factor networks, including those in yeast, flies and mammals.http://europepmc.org/articles/PMC4222607?pdf=render |
| spellingShingle | Ricardo Pinho Victor Garcia Manuel Irimia Marcus W Feldman Stability depends on positive autoregulation in Boolean gene regulatory networks. PLoS Computational Biology |
| title | Stability depends on positive autoregulation in Boolean gene regulatory networks. |
| title_full | Stability depends on positive autoregulation in Boolean gene regulatory networks. |
| title_fullStr | Stability depends on positive autoregulation in Boolean gene regulatory networks. |
| title_full_unstemmed | Stability depends on positive autoregulation in Boolean gene regulatory networks. |
| title_short | Stability depends on positive autoregulation in Boolean gene regulatory networks. |
| title_sort | stability depends on positive autoregulation in boolean gene regulatory networks |
| url | http://europepmc.org/articles/PMC4222607?pdf=render |
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