Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen Darach Miller Nathan Brandt David Gresham 10.1371/journal.pgen.1007406 https://plos.figshare.com/articles/dataset/Systematic_identification_of_factors_mediating_accelerated_mRNA_degradation_in_response_to_changes_in_environmental_nitrogen/6296768 <div><p>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 <i>Saccharomyces cerevisiae</i> 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 <i>trans</i> factors that mediate rapid <i>GAP1</i> mRNA repression. We combined low-input multiplexed <u>B</u>arcode sequencing with branched-DNA single-molecule mRNA <u>F</u>ISH and <u>F</u>luorescence-activated cell sorting (BFF) to identify the Lsm1-7p/Pat1p complex and general mRNA decay machinery as important for <i>GAP1</i> mRNA clearance. We also find that the decapping modulators <i>EDC3</i> and <i>SCD6</i>, translation factor eIF4G2, and the 5’ UTR of <i>GAP1</i> are factors that mediate rapid repression of <i>GAP1</i> mRNA, suggesting that translational control may impact the post-transcriptional fate of mRNAs in response to environmental changes.</p></div> 2018-05-21 17:44:02 Lsm 1-7p nitrogen Cellular responses deletion collection library mRNA stability mRNA degradation rates mRNA destabilization yeast Saccharomyces cerevisiae branched-DNA single-molecule mRNA F ISH low-input multiplexed B arcode sequencing decapping modulators EDC 3 GAP 1 mRNA repression 78 mRNAs SortSeq approach GAP 1 mRNA translation factor eIF 4G Regulated changes F luorescence-activated cell GAP 1 mRNA clearance mRNA decay machinery carbon metabolism mRNAs SCD 6 nitrogen upshift GAP 1 translational control BFF trans factors 4- thiouracil post-transcriptional fate Nitrogen Catabolite Repression UTR NCR mRNA degradation Systematic identification