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Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress.
- Source :
-
Nature communications [Nat Commun] 2017 Apr 11; Vol. 8 (1), pp. 12. Date of Electronic Publication: 2017 Apr 11. - Publication Year :
- 2017
-
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.
- Subjects :
- Culture Media pharmacology
DNA, Complementary genetics
DNA, Complementary metabolism
Gene Expression Profiling
Glucose deficiency
Kinetics
Nuclear Proteins metabolism
Protein Binding
RNA, Fungal metabolism
RNA-Binding Proteins metabolism
Saccharomyces cerevisiae drug effects
Saccharomyces cerevisiae metabolism
Saccharomyces cerevisiae radiation effects
Saccharomyces cerevisiae Proteins metabolism
Stress, Physiological
Time Factors
Ultraviolet Rays
Gene Expression Regulation, Fungal
Nuclear Proteins genetics
RNA, Fungal genetics
RNA-Binding Proteins genetics
Saccharomyces cerevisiae genetics
Saccharomyces cerevisiae Proteins genetics
Transcriptome
Subjects
Details
- Language :
- English
- ISSN :
- 2041-1723
- Volume :
- 8
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Nature communications
- Publication Type :
- Academic Journal
- Accession number :
- 28400552
- Full Text :
- https://doi.org/10.1038/s41467-017-00025-5