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Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

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  • Christina Kahramanoglou

    (University of Cambridge
    MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.)

  • Ana I. Prieto

    (University of Cambridge
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
    EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus)

  • Supriya Khedkar

    (National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK)

  • Bettina Haase

    (Genomics Core Facility, European Molecular Biology Laboratory)

  • Ankur Gupta

    (National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK)

  • Vladimir Benes

    (Genomics Core Facility, European Molecular Biology Laboratory)

  • Gillian M. Fraser

    (University of Cambridge)

  • Nicholas M. Luscombe

    (EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus
    Okinawa Institute of Science and Technology, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan.
    UCL Genetics Institute, Environment and Evolution, University College London
    Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields)

  • Aswin S.N. Seshasayee

    (National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK)

Abstract

DNA cytosine methylation regulates gene expression in mammals. In bacteria, its role in gene expression and genome architecture is less understood. Here we perform high-throughput sequencing of bisulfite-treated genomic DNA from Escherichia coli K12 to describe, for the first time, the extent of cytosine methylation of bacterial DNA at single-base resolution. Whereas most target sites (CmCWGG) are fully methylated in stationary phase cells, many sites with an extended CCmCWGG motif are only partially methylated in exponentially growing cells. We speculate that these partially methylated sites may be selected, as these are slightly correlated with the risk of spontaneous, non-synonymous conversion of methylated cytosines to thymines. Microarray analysis in a cytosine methylation-deficient mutant of E. coli shows increased expression of the stress response sigma factor RpoS and many of its targets in stationary phase. Thus, DNA cytosine methylation is a regulator of stationary phase gene expression in E. coli.

Suggested Citation

  • Christina Kahramanoglou & Ana I. Prieto & Supriya Khedkar & Bettina Haase & Ankur Gupta & Vladimir Benes & Gillian M. Fraser & Nicholas M. Luscombe & Aswin S.N. Seshasayee, 2012. "Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription," Nature Communications, Nature, vol. 3(1), pages 1-9, January.
    • Handle: RePEc:nat:natcom:v:3:y:2012:i:1:d:10.1038_ncomms1878
    DOI: 10.1038/ncomms1878
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