Protocols for Probing Genome Architecture of Regulatory Networks in Hydrocarbon and Lipid Microorganisms

  • Costas Bouyioukos
  • Mohamed Elati
  • François KépèsEmail author
Part of the Springer Protocols Handbooks book series (SPH)


Genome architecture and the regulation of gene expression are expected to be interdependent. Understanding this interdependence is key to successful genome engineering. Evidence for nonrandom arrangement of genes along genomes, defined as the relative positioning of cofunctional or co-regulated genes, stems from two main approaches. Firstly, the analysis of contiguous genome segments across species has highlighted the conservation of gene order (synteny) along chromosome regions. Secondly, the study of long-range regularities along chromosomes of one given species has emphasised periodic positioning of microbial genes that are either co-regulated, evolutionarily correlated, or highly codon biased. Software tools to detect, visualise, systematically analyse and exploit gene position regularities along genomes can facilitate the studies of such nonrandom genome layouts and the inference of transcription factor binding sites and potentially guide rational genome design. Here, a computational protocol is demonstrated for the analysis and exploitation of regular patterns in a set of genomic features of interest (e.g. cofunctional or co-regulated genes, chromatin immunoprecipitation results, etc.). This case study is conducted for genes involved in hydrocarbon metabolism of a marine petroleum-degrading bacterium Alcanivorax borkumensis.


Gene regulation Genome architecture Genome organisation Periodicity detection Prediction of TFBSs 



The authors thank the MEGA team members at iSSB for excellent discussions. This work was supported by Genopole, by the OSEO/BPI-France ‘BioIntelligence’ consortium and by the EU FP7 KBBE project ‘ST-FLOW’.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Costas Bouyioukos
    • 1
  • Mohamed Elati
    • 1
  • François Képès
    • 1
    • 2
    Email author
  1. 1.Institute of Systems and Synthetic Biology, Genopole, CNRS, University of EvryEvryFrance
  2. 2.Department of BioEngineeringImperial College LondonLondonUK

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