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Series GSE86483 Query DataSets for GSE86483
Status Public on Jan 01, 2017
Title Nuclear RNA decay pathways aid rapid remodeling of gene expression in yeast
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary In budding yeast, the nuclear RNA surveillance system is active on all pre-mRNA transcripts and modulated by nutrient availability. To test the role of nuclear surveillance in reprograming gene expression, we identified transcriptome-wide binding sites for RNA polymerase II (Pol II) and the exosome cofactors Mtr4 (TRAMP complex) and Nab3 (NNS complex) by UV-crosslinking immediately following glucose withdrawal (0, 4, and 8 minutes). In glucose, mRNA binding by Nab3 and Mtr4 was mainly restricted to promoter-proximal sites, reflecting early transcription termination. Following glucose withdrawal, many mRNAs showed reduced transcription but increased Nab3 binding, accompanied by downstream recruitment of Mtr4, and oligo(A) tailing. This indicates transcription termination followed by TRAMP-mediated RNA decay. Upregulated transcripts generally showed low or strongly reduced binding of Nab3 and Mtr4. We conclude that nuclear surveillance pathways regulate both positive and negative responses to glucose availability.
Overall design CRAC datasets were collected for Rpo21, Nab3, and Mtr4 at 0, 4, and 8 minutes. Total RNA was measured by RNA-seq at 0, 8, and 16 minutes following glucose starvation.
Contributor(s) Bresson S, Tuck A, Staneva D, Tollervey D
Citation(s) 28190770
Submission date Sep 06, 2016
Last update date May 15, 2019
Contact name Stefan Bresson
Organization name University of Edinburgh
Department Wellcome Trust Centre for Cell Biology
Lab Tollervey Lab
Street address Max Born Crescent, Swann 5.1
City Edinburgh
State/province Scotland
ZIP/Postal code EH9 3BF
Country United Kingdom
Platforms (1)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (24)
GSM2304404 Rpo21_0_replicate1
GSM2304405 Rpo21_0_replicate2
GSM2304406 Rpo21_8_replicate1
BioProject PRJNA342024
SRA SRP086811

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Supplementary file Size Download File type/resource
GSE86483_RAW.tar 191.7 Mb (http)(custom) TAR (of BEDGRAPH, BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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