title: Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress.
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.Protein RNA interactions are dynamic and regulated in response to environmental changes. Here the authors describe 'kinetic CRAC', an approach that allows time resolved analyses of protein RNA interactions with minute time point resolution and apply it to gain insight into the function of the RNA-binding protein Nab3.
authors.affiliation: Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3BF, UK.|Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK.
authors.forename: Rob
authors.initials: R
authors.lastname: van Nues
authors.affiliation: School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, UK.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Schweikert
authors.affiliation: Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3BF, UK.|Institute for Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
authors.forename: Erica
authors.initials: E
authors.lastname: de Leau
authors.affiliation: School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, UK.
authors.forename: Alina
authors.initials: A
authors.lastname: Selega
authors.affiliation: UVO3 Ltd, Unit 25 Stephenson Road, St Ives, Cambridgeshire, PE27 3WJ, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Langford
authors.affiliation: UVO3 Ltd, Unit 25 Stephenson Road, St Ives, Cambridgeshire, PE27 3WJ, UK.
authors.forename: Ryan
authors.initials: R
authors.lastname: Franklin
authors.affiliation: Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3BF, UK.
authors.forename: Ira
authors.initials: I
authors.lastname: Iosub
authors.affiliation: UVO3 Ltd, Unit 25 Stephenson Road, St Ives, Cambridgeshire, PE27 3WJ, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Wadsworth
authors.affiliation: Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3BF, UK.|School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, UK.
authors.forename: Guido
authors.initials: G
authors.lastname: Sanguinetti
authors.affiliation: Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3BF, UK. sgrannem@staffmail.ed.ac.uk.
authors.forename: Sander
authors.identifier: http://orcid.org/0000-0003-4387-1271
authors.initials: S
authors.lastname: Granneman
mesh_terms: D003470:Culture Media / Q000494:pharmacology; D018076:DNA, Complementary / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D005947:Glucose / Q000172:deficiency; D007700:Kinetics; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism; D011485:Protein Binding; D012331:RNA, Fungal / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism / Q000528:radiation effects; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D013312:Stress, Physiological; D013997:Time Factors; D059467:Transcriptome; D014466:Ultraviolet Rays
chemical_list: D003470:Culture Media; D018076:DNA, Complementary; C090564:NAB3 protein, S cerevisiae; D009687:Nuclear Proteins; D012331:RNA, Fungal; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D005947:Glucose