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

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

Abstract

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.

Keywords:

Gene regulation Genome architecture Genome organisation Periodicity detection Prediction of TFBSs 

References

  1. 1.
    Huynen MA, van Nimwegen E (1998) The frequency distribution of gene family sizes in complete genomes. Mol Biol Evol 15(5):583–589CrossRefPubMedGoogle Scholar
  2. 2.
    Dorman CJ (2013) Genome architecture and global gene regulation in bacteria: making progress towards a unified model? Nat Rev Microbiol 11:349–355CrossRefPubMedGoogle Scholar
  3. 3.
    Képès F, Vaillant C (2003) Transcription-based solenoidal model of chromosomes. ComPlexUs 1:171–180CrossRefGoogle Scholar
  4. 4.
    Képès F (2004) Periodic transcriptional organization of the E.coli genome. J Mol Biol 340:957–964CrossRefPubMedGoogle Scholar
  5. 5.
    Képès F (2003) Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites. J Mol Biol 329:859–865CrossRefPubMedGoogle Scholar
  6. 6.
    Junier I, Hérisson J, Képès F (2012) Genomic organization of evolutionarily correlated genes in bacteria: limits and strategies. J Mol Biol 419:369–386CrossRefPubMedGoogle Scholar
  7. 7.
    Wright MA, Kharchenko P, Church GM, Segré D (2007) Chromosomal periodicity of evolutionarily conserved gene pairs. Proc Natl Acad Sci U S A 104:10559–10564CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Ma Q, Ying X (2013) Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency. Genomics Proteomics Bioinformatics 11:66–71CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Porcar M, Danchin A, de Lorenzo V (2014) Confidence, tolerance, and allowance in biological engineering: the nuts and bolts of living things. Bioessays 37:95–102CrossRefPubMedGoogle Scholar
  10. 10.
    Junier I, Hérisson J, Képès F (2010) Periodic pattern detection in sparse boolean sequences. Algorithms Mol Biol 5:31CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Elati M, Fekih R, Nicolle R, Junier I, Herisson J, Képès F (2011) Boosting binding sites prediction using gene’s positions. In: Algorithms in bioinformatics (WABI’11), LNCS – 6833, pp 92–103Google Scholar
  12. 12.
    Elati M, Nicolle R, Junier I, Fernández D, Fekih R, Font J, Képès F (2013) PreCisIon: PREdiction of CIS-regulatory elements improved by gene’s positION. Nucleic Acids Res 41(3):1406–1415CrossRefPubMedGoogle Scholar
  13. 13.
    Turatsinze JV, Thomas-Chollier M, Defrance M, van Helden J (2008) Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc 3(10):1578–1588CrossRefPubMedGoogle Scholar
  14. 14.
    Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J (2013) RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res 41:D203–D213CrossRefPubMedGoogle Scholar
  15. 15.
    Schneiker S, Martins dos Santos VAP, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter F-J, Weidner S, Kaiser O, Golyshin PN (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 24:997–1004CrossRefPubMedGoogle Scholar
  16. 16.
    Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM (2006) The UCSC archaeal genome browser. Nucleic Acids Res 34:D407–D410CrossRefPubMedGoogle Scholar
  17. 17.
    Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J (2000) Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci U S A 97:6652–6657CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Ester M, Kriegel H, Sander J, Xu X (1996). A density-based algorithm for discovering clusters in large spatial databases with noise. In: Simoudis E, Han J, Fayyad UM (eds) Proceedings of the second international conference on knowledge discovery and data mining (KDD-96), Portland. AAAI, pp 226–231Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

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

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