Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen

Darach Miller, Nathan Brandt, David Gresham

Research output: Contribution to journalArticle

Abstract

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 of the transcriptome. To explore the molecular basis of destabilization we implemented a SortSeq approach to screen 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 the Lsm1-7p/Pat1p complex and general mRNA decay machinery as important for GAP1 mRNA clearance. We also find that the decapping modulators EDC3 and SCD6, translation factor eIF4G2, and the 5’ UTR of GAP1 are factors that mediate rapid repression of GAP1 mRNA, suggesting that translational control may impact the post-transcriptional fate of mRNAs in response to environmental changes.

Original languageEnglish (US)
Article numbere1007406
JournalPLoS Genetics
Volume14
Issue number5
DOIs
StatePublished - May 1 2018

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RNA Stability
transcriptome
Nitrogen
thiouracil
Messenger RNA
degradation
barcoding
nitrogen
5' untranslated regions
translation (genetics)
flow cytometry
Saccharomyces cerevisiae
deterioration
metabolites
yeasts
machinery
sorting
metabolism
yeast
carbon

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

Cite this

Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen. / Miller, Darach; Brandt, Nathan; Gresham, David.

In: PLoS Genetics, Vol. 14, No. 5, e1007406, 01.05.2018.

Research output: Contribution to journalArticle

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