Universal attenuators and their interactions with feedback loops in gene regulatory networks

Dianbo Liu, Luca Albergante, Timothy J. Newman (Lead / Corresponding author)

Research output: Contribution to journalArticle

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Abstract

Using a combination of mathematical modelling, statistical simulation and large-scale data analysis we study the properties of linear regulatory chains (LRCs) within gene regulatory networks (GRNs). Our modelling indicates that downstream genes embedded within LRCs are highly insulated from the variation in expression of upstream genes, and thus LRCs act as attenuators. This observation implies a progressively weaker functionality of LRCs as their length increases. When analyzing the preponderance of LRCs in the GRNs of Escherichia coli K12 and several other organisms, we find that very long LRCs are essentially absent. In both E. coli and M. tuberculosis we find that four-gene LRCs are intimately linked to identical feedback loops that are involved in potentially chaotic stress response, indicating that the dynamics of these potentially destabilising motifs are strongly restrained under homeostatic conditions. The same relationship is observed in a human cancer cell line (K562), and we postulate that four-gene LRCs act as 'universal attenuators'. These findings suggest a role for long LRCs in dampening variation in gene expression, thereby protecting cell identity, and in controlling dramatic shifts in cell-wide gene expression through inhibiting chaos-generating motifs.

Original languageEnglish
Pages (from-to)7078-7093
Number of pages16
JournalNucleic Acids Research
Volume45
Issue number12
Early online date1 Jun 2017
DOIs
Publication statusPublished - 7 Jul 2017

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Gene Regulatory Networks
Regulator Genes
Gene Expression
Escherichia coli K12
Tuberculosis
Escherichia coli
Cell Line
Genes
Neoplasms

Keywords

  • feedback
  • genes
  • mathematics
  • tuberculosis

Cite this

Liu, Dianbo ; Albergante, Luca ; Newman, Timothy J. / Universal attenuators and their interactions with feedback loops in gene regulatory networks. In: Nucleic Acids Research. 2017 ; Vol. 45, No. 12. pp. 7078-7093.
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Universal attenuators and their interactions with feedback loops in gene regulatory networks. / Liu, Dianbo; Albergante, Luca; Newman, Timothy J. (Lead / Corresponding author).

In: Nucleic Acids Research, Vol. 45, No. 12, 07.07.2017, p. 7078-7093.

Research output: Contribution to journalArticle

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T1 - Universal attenuators and their interactions with feedback loops in gene regulatory networks

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