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Global repositioning of transcription start sites in a plant-fermenting bacterium

Author

Listed:
  • Magali Boutard

    (1CEA, DRF, IG, Genoscope
    CNRS-UMR8030)

  • Laurence Ettwiller

    (New England Biolabs, Inc.)

  • Tristan Cerisy

    (1CEA, DRF, IG, Genoscope
    CNRS-UMR8030
    Université Paris-Saclay
    Université d'Évry)

  • Adriana Alberti

    (1CEA, DRF, IG, Genoscope)

  • Karine Labadie

    (1CEA, DRF, IG, Genoscope)

  • Marcel Salanoubat

    (1CEA, DRF, IG, Genoscope
    CNRS-UMR8030
    Université Paris-Saclay
    Université d'Évry)

  • Ira Schildkraut

    (New England Biolabs, Inc.)

  • Andrew C. Tolonen

    (1CEA, DRF, IG, Genoscope
    CNRS-UMR8030
    Université Paris-Saclay
    Université d'Évry)

Abstract

Bacteria respond to their environment by regulating mRNA synthesis, often by altering the genomic sites at which RNA polymerase initiates transcription. Here, we investigate genome-wide changes in transcription start site (TSS) usage by Clostridium phytofermentans, a model bacterium for fermentation of lignocellulosic biomass. We quantify expression of nearly 10,000 TSS at single base resolution by Capp-Switch sequencing, which combines capture of synthetically capped 5′ mRNA fragments with template-switching reverse transcription. We find the locations and expression levels of TSS for hundreds of genes change during metabolism of different plant substrates. We show that TSS reveals riboswitches, non-coding RNA and novel transcription units. We identify sequence motifs associated with carbon source-specific TSS and use them for regulon discovery, implicating a LacI/GalR protein in control of pectin metabolism. We discuss how the high resolution and specificity of Capp-Switch enables study of condition-specific changes in transcription initiation in bacteria.

Suggested Citation

  • Magali Boutard & Laurence Ettwiller & Tristan Cerisy & Adriana Alberti & Karine Labadie & Marcel Salanoubat & Ira Schildkraut & Andrew C. Tolonen, 2016. "Global repositioning of transcription start sites in a plant-fermenting bacterium," Nature Communications, Nature, vol. 7(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13783
    DOI: 10.1038/ncomms13783
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