PT  - JOURNAL ARTICLE
AU  - Darach Miller
AU  - Nathan Brandt
AU  - David Gresham
TI  - Global analysis of gene expression dynamics identifies factors required for accelerated mRNA degradation
AID  - 10.1101/254920
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 254920
4099  - http://biorxiv.org/content/early/2018/01/29/254920.short
4100  - http://biorxiv.org/content/early/2018/01/29/254920.full
AB  - Cellular responses to changing environments frequently involve rapid reprogramming of the transcriptome. Regulated changes in mRNA degradation rates can accelerate reprogramming by clearing or stabilizing extant transcripts. Here, we measured mRNA stability using 4-thiouracil labeling in the budding yeast Saccharomyces cerevisiae during a nitrogen upshift and found that 78 mRNAs are subject to destabilization. These transcripts include Nitrogen Catabolite Repression (NCR) and carbon metabolism mRNAs, suggesting that mRNA destabilization is a mechanism for targeted reprogramming. To explore the molecular basis of destabilization we implemented a SortSeq approach to screen using the pooled deletion collection library for trans factors that mediate rapid GAP1 mRNA repression. We combined low-input multiplexed Barcode sequencing with branched-DNA single-molecule mRNA FISH and Fluorescence-activated cell sorting (BFF) to identify that the Lsm1-7p/Pat1p complex and general mRNA decay machinery are important for GAP1 mRNA clearance. We also find that the decapping modulator SCD6, translation factor eIF4G2, and the 5’ UTR of GAP1 are important for this repression, suggesting that translational control may impact the post-transcriptional fate of mRNAs in response to environmental changes.