Su et al. 2018 (PRJNA397035)

General Details

Title Ribosome profiling analysis of heat effect on rice
Organism
Number of Samples 4
Release Date 2017/08/03 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP114761
ENA SRP114761
GEO
BioProject PRJNA397035

Publication

Title
Authors Su Z,Tang Y,Ritchey LE,Tack DC,Zhu M,Bevilacqua PC,Assmann SM
Journal Proceedings of the National Academy of Sciences of the United States of America
Publication Date 2018 Nov 27
Abstract The heat shock response is crucial for organism survival in natural environments. RNA structure is known to influence numerous processes related to gene expression, but there have been few studies on the global RNA structurome as it prevails in vivo. Moreover, how heat shock rapidly affects RNA structure genome-wide in living systems remains unknown. We report here in vivo heat-regulated RNA structuromes. We applied Structure-seq chemical [dimethyl sulfate (DMS)] structure probing to rice ( Oryza sativa L.) seedlings with and without 10 min of 42 °C heat shock and obtained structural data on >14,000 mRNAs. We show that RNA secondary structure broadly regulates gene expression in response to heat shock in this essential crop species. Our results indicate significant heat-induced elevation of DMS reactivity in the global transcriptome, revealing RNA unfolding over this biological temperature range. Our parallel Ribo-seq analysis provides no evidence for a correlation between RNA unfolding and heat-induced changes in translation, in contrast to the paradigm established in prokaryotes, wherein melting of RNA thermometers promotes translation. Instead, we find that heat-induced DMS reactivity increases correlate with significant decreases in transcript abundance, as quantified from an RNA-seq time course, indicating that mRNA unfolding promotes transcript degradation. The mechanistic basis for this outcome appears to be mRNA unfolding at both 5' and 3'-UTRs that facilitates access to the RNA degradation machinery. Our results thus reveal unexpected paradigms governing RNA structural changes and the eukaryotic RNA life cycle. Copyright © 2018 the Author(s). Published by PNAS.
PMC PMC6275526
PMID 30413617
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR5892473 PRJNA397035 Oryza sativa Ribo-Seq
SRR5892474 PRJNA397035 Oryza sativa Ribo-Seq
SRR5892475 PRJNA397035 Oryza sativa Ribo-Seq
SRR5892476 PRJNA397035 Oryza sativa Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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