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