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

Rob van Nues, Gabriele Schweikert, Erica de Leau, Alina Selega, Andrew Langford, Ryan Franklin, Ira Iosub, Peter Wadsworth, Guido Sanguinetti and Sander Granneman ()
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Rob van Nues: University of Edinburgh
Gabriele Schweikert: University of Edinburgh
Erica de Leau: 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
Sander Granneman: University of Edinburgh

Nature Communications, 2017, vol. 8, issue 1, 1-18

Abstract: 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.

Date: 2017
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DOI: 10.1038/s41467-017-00025-5

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