ArticlePLoS genetics2018
Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
10 citing papers in PubMed, 141 citations in OpenAlex.
- Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression.bioRxiv : the preprint server for biology · 2023Article
- Global SLAM-seq for accurate mRNA decay determination and identification of NMD targets.RNA (New York, N.Y.) · 2022Article
- Advances in automated real-time flow cytometry for monitoring of bioreactor processes.Engineering in life sciences · 2022Review
- Dynamic post-transcriptional regulation by Mrn1 links cell wall homeostasis to mitochondrial structure and function.PLoS genetics · 2021Article
- Genome-wide analysis of lncRNA stability in human.PLoS computational biology · 2021Article
- Article
- Control of Translation at the Initiation Phase During Glucose Starvation in Yeast.International journal of molecular sciences · 2019Review
- RNA polymerase II ChIP-seq-a powerful and highly affordable method for studying fungal genomics and physiology.Biophysical reviews · 2019Article
- Transcription-dependent spreading of the Dal80 yeast GATA factor across the body of highly expressed genes.PLoS genetics · 2019Article
- Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine.Wiley interdisciplinary reviews. RNA · 2019Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.