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Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress

Author

Listed:
  • Rob van Nues

    (University of Edinburgh
    University of Edinburgh)

  • Gabriele Schweikert

    (University of Edinburgh)

  • Erica de Leau

    (University of Edinburgh
    University of Edinburgh)

  • Alina Selega

    (University of Edinburgh)

  • Andrew Langford

    (UVO3 Ltd)

  • Ryan Franklin

    (UVO3 Ltd)

  • Ira Iosub

    (University of Edinburgh)

  • Peter Wadsworth

    (UVO3 Ltd)

  • Guido Sanguinetti

    (University of Edinburgh
    University of Edinburgh)

  • Sander Granneman

    (University of Edinburgh)

Abstract

RNA-binding proteins play a key role in shaping gene expression profiles during stress, however, little is known about the dynamic nature of these interactions and how this influences the kinetics of gene expression. To address this, we developed kinetic cross-linking and analysis of cDNAs (χCRAC), an ultraviolet cross-linking method that enabled us to quantitatively measure the dynamics of protein–RNA interactions in vivo on a minute time-scale. Here, using χCRAC we measure the global RNA-binding dynamics of the yeast transcription termination factor Nab3 in response to glucose starvation. These measurements reveal rapid changes in protein–RNA interactions within 1 min following stress imposition. Changes in Nab3 binding are largely independent of alterations in transcription rate during the early stages of stress response, indicating orthogonal transcriptional control mechanisms. We also uncover a function for Nab3 in dampening expression of stress-responsive genes. χCRAC has the potential to greatly enhance our understanding of in vivo dynamics of protein–RNA interactions.

Suggested Citation

  • Rob van Nues & Gabriele Schweikert & Erica de Leau & Alina Selega & Andrew Langford & Ryan Franklin & Ira Iosub & Peter Wadsworth & Guido Sanguinetti & Sander Granneman, 2017. "Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress," Nature Communications, Nature, vol. 8(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-00025-5
    DOI: 10.1038/s41467-017-00025-5
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    Cited by:

    1. Ross A. Cordiner & Yuhui Dou & Rune Thomsen & Andrii Bugai & Sander Granneman & Torben Heick Jensen, 2023. "Temporal-iCLIP captures co-transcriptional RNA-protein interactions," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Daniel G. Mediati & Julia L. Wong & Wei Gao & Stuart McKellar & Chi Nam Ignatius Pang & Sylvania Wu & Winton Wu & Brandon Sy & Ian R. Monk & Joanna M. Biazik & Marc R. Wilkins & Benjamin P. Howden & T, 2022. "RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Liang-Cui Chu & Pedro Arede & Wei Li & Erika C. Urdaneta & Ivayla Ivanova & Stuart W. McKellar & Jimi C. Wills & Theresa Fröhlich & Alexander Kriegsheim & Benedikt M. Beckmann & Sander Granneman, 2022. "The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins," Nature Communications, Nature, vol. 13(1), pages 1-18, December.

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