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A system-level model for the microbial regulatory genome.

Aaron N Brooks1, David J Reiss2, Antoine Allard3

  • 1Institute for Systems Biology, Seattle, WA, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.

Molecular Systems Biology
|July 17, 2014
PubMed
Summary
This summary is machine-generated.

This study models microbial gene regulation in Escherichia coli and Halobacterium salinarum, revealing how genome organization and transcription factors create environment-specific responses. These findings define a new principle for prokaryotic gene regulatory networks.

Keywords:
EGRINgene regulatory networkssystems biologytranscriptional regulation

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Area of Science:

  • Microbiology
  • Systems Biology
  • Genomics

Background:

  • Microbes adapt to environmental changes using transcriptional responses.
  • Prokaryotic genomes are streamlined with limited regulators.

Purpose of the Study:

  • To develop data-driven models of gene regulation in Escherichia coli and Halobacterium salinarum.
  • To understand how environmental factors and genome-encoded regulators interact.
  • To uncover a generalized organizing principle for prokaryotic gene regulatory networks.

Main Methods:

  • Development of data-driven computational models.
  • Analysis of genome-wide distributions of cis-acting gene regulatory elements.
  • Modeling conditional transcription factor influences.

Main Results:

  • Models capture dynamic interplay between environment and regulatory programs.
  • Demonstrated partitioning of transcriptional regulation within regulons and operons.
  • Revealed re-organization of gene-gene functional associations based on environment.
  • Identified fitness-relevant co-regulation across the genome.

Conclusions:

  • A generalized, system-level organizing principle for prokaryotic gene regulatory networks was defined.
  • The models go beyond existing paradigms of gene regulation.
  • An online resource facilitates exploration of conditional gene regulation.