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Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation

In this paper, a new model of self-organized criticality is introduced. This model, called the gene expression paradigm, is motivated by the problem of gene expression initiation in the newly-born daughter cells after mitosis. The model is fundamentally different in dynamics and properties from the...

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Detalles Bibliográficos
Autor principal: Rosenfeld, Simon
Formato: Texto
Lenguaje:English
Publicado: Libertas Academica 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080741/
https://www.ncbi.nlm.nih.gov/pubmed/21523248
http://dx.doi.org/10.4137/GRSB.S6804
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author Rosenfeld, Simon
author_facet Rosenfeld, Simon
author_sort Rosenfeld, Simon
collection PubMed
description In this paper, a new model of self-organized criticality is introduced. This model, called the gene expression paradigm, is motivated by the problem of gene expression initiation in the newly-born daughter cells after mitosis. The model is fundamentally different in dynamics and properties from the well known sand-pile paradigm. Simulation experiments demonstrate that a critical total number of proteins exists below which transcription is impossible. Above this critical threshold, the system enters the regime of self-sustained oscillations with standard deviations and periods proportional to the genes’ complexities with probability one. The borderline between these two regimes is very sharp. Importantly, such a self-organization emerges without any deterministic feedback loops or external supervision, and is a result of completely random redistribution of proteins between inactive genes. Given the size of the genome, the domain of self-organized oscillatory motion is also limited by the genes’ maximal complexities. Below the critical complexity, all the regimes of self-organized oscillations are self-similar and largely independent of the genes’ complexities. Above the level of critical complexity, the whole-genome transcription is impossible. Again, the borderline between the domains of oscillations and quiescence is very sharp. The gene expression paradigm is an example of cellular automata with the domain of application potentially far beyond its biological context. The model seems to be simple enough for staging an experiment for verification of its remarkable properties.
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spelling pubmed-30807412011-04-26 Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation Rosenfeld, Simon Gene Regul Syst Bio Original Research In this paper, a new model of self-organized criticality is introduced. This model, called the gene expression paradigm, is motivated by the problem of gene expression initiation in the newly-born daughter cells after mitosis. The model is fundamentally different in dynamics and properties from the well known sand-pile paradigm. Simulation experiments demonstrate that a critical total number of proteins exists below which transcription is impossible. Above this critical threshold, the system enters the regime of self-sustained oscillations with standard deviations and periods proportional to the genes’ complexities with probability one. The borderline between these two regimes is very sharp. Importantly, such a self-organization emerges without any deterministic feedback loops or external supervision, and is a result of completely random redistribution of proteins between inactive genes. Given the size of the genome, the domain of self-organized oscillatory motion is also limited by the genes’ maximal complexities. Below the critical complexity, all the regimes of self-organized oscillations are self-similar and largely independent of the genes’ complexities. Above the level of critical complexity, the whole-genome transcription is impossible. Again, the borderline between the domains of oscillations and quiescence is very sharp. The gene expression paradigm is an example of cellular automata with the domain of application potentially far beyond its biological context. The model seems to be simple enough for staging an experiment for verification of its remarkable properties. Libertas Academica 2011-03-22 /pmc/articles/PMC3080741/ /pubmed/21523248 http://dx.doi.org/10.4137/GRSB.S6804 Text en © the author(s), publisher and licensee Libertas Academica Ltd. This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.
spellingShingle Original Research
Rosenfeld, Simon
Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation
title Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation
title_full Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation
title_fullStr Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation
title_full_unstemmed Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation
title_short Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation
title_sort critical self-organized self-sustained oscillations in large regulatory networks: towards understanding the gene expression initiation
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080741/
https://www.ncbi.nlm.nih.gov/pubmed/21523248
http://dx.doi.org/10.4137/GRSB.S6804
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