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, Sander Granneman (Lead / Corresponding author)

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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.

Original languageEnglish
Article number12
JournalNature Communications
Volume8
Issue number1
DOIs
Publication statusPublished - 11 Apr 2017

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    Van Nues, R., Schweikert, G., De Leau, E., Selega, A., Langford, A., Franklin, R., Iosub, I., Wadsworth, P., Sanguinetti, G., & Granneman, S. (2017). Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress. Nature Communications, 8(1), [12]. https://doi.org/10.1038/s41467-017-00025-5