Widespread suppression of intragenic transcription initiation by H-NS

  1. David C. Grainger1,5
  1. 1Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom:
  2. 2Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA;
  3. 3Department of Biomedical Sciences, University at Albany, Albany, New York 12201, USA
    1. 4 These authors contributed equally to this work.

    Abstract

    Widespread intragenic transcription initiation has been observed in many species. Here we show that the Escherichia coli ehxCABD operon contains numerous intragenic promoters in both sense and antisense orientations. Transcription from these promoters is silenced by the histone-like nucleoid structuring (H-NS) protein. On a genome-wide scale, we show that 46% of H-NS-suppressed transcripts in E. coli are intragenic in origin. Furthermore, many intergenic promoters repressed by H-NS are for noncoding RNAs (ncRNAs). Thus, a major overlooked function of H-NS is to prevent transcription of spurious RNA. Our data provide a molecular description for the toxicity of horizontally acquired DNA and explain how this is counteracted by H-NS.

    Keywords

    Footnotes

    • 5 Corresponding authors

      E-mail d.grainger{at}bham.ac.uk

      E-mail jwade{at}wadsworth.org

    • Supplemental material is available for this article.

    • Article published online ahead of print. Article and publication date are online at http://www.genesdev.org/cgi/doi/10.1101/gad.234336.113.

      Freely available online through the Genes & Development Open Access option.

    • Received November 6, 2013.
    • Accepted December 17, 2013.

    This article, published in Genes & Development, is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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