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SRX24354542: GSM8228792: Zebrafish, RNAseq, high dose, uninj2; Danio rerio; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 19.5M spots, 5.8G bases, 1.8Gb downloads

External Id: GSM8228792_r1
Submitted by: Shandong University
Study: Double-stranded RNA triggers a distinct integrated stress response in the early embryo [RNA-seq, Ribo-seq]
show Abstracthide Abstract
Double-stranded RNA (dsRNA) is associated with virus infections and is present as by-products during the transcription of synthetic mRNA, which has been widely used in gene gain-of-function studies and serves as a core component in emerging mRNA-based therapies1-4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5,6. Unlike differentiated cells, undifferentiated cells adopt a distinct defense strategy against RNA virus infection7, but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR-eIF2a independent manner and leads to developmental delay and cell necrosis, it also strongly induces p53 activation, which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly, we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA-induced stress response in the embryo, reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution. Overall design: To characterize the distribution of ribosomes on mRNA, we performed Ribosome profiling (Ribo-seq) analysis with RNA-seq on dsRNA-injected embryos.
Sample: Zebrafish, RNAseq, high dose, uninj2
SAMN41071440 • SRS21112308 • All experiments • All runs
Organism: Danio rerio
Library:
Name: GSM8228792
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Total RNAs were extracted from 6 hpf embryos using TRIzol reagent (Invitrogen), and were precipitated by cold isopropanol (50%, v/v) in the presence of carrier glycogen (20 µg/each sample). Polyadenylated mRNAs were purified by the poly(A) mRNA Magnetic Isolation Module (NEB). The mRNA libraries were then generated using NEBNext Ultra RNA Library Prep Kit for lllumina following manufacturer's instruction. Briefly, mRNA fragmentation and priming were carried out via NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. ProtoScript II Reverse Transcriptase and Second Strand Synthesis Enzyme Mix were used to synthesize first and second strand cDNAs. AxyPrep Mag PCR Clean-up (Axygen) kit were then used to purify the cDNAs. After that, cDNAs were treated with End Prep Enzyme Mix to repair 3' and 5' ends, followed by dA-tailing and adaptor ligation. Following size selection by AxyPrep Mag PCR Clean-up (Axygen) kit, fragments haboring around 300 bp inserts were recovered.
Runs: 1 run, 19.5M spots, 5.8G bases, 1.8Gb
Run# of Spots# of BasesSizePublished
SRR2879026219,450,4465.8G1.8Gb2024-04-26

ID:
32669198

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