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The integrated stress response finetunes 18S nonfunctional rRNA decay (DMS-MaPseq)

ABSTRACT: The integrated stress response finetunes 18S nonfunctional rRNA decay (DMS-MaPseq)

PROVIDER: PRJNA1076513 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27968057.fastq.gz	Fastqsanger.gz
	SRR27968058.fastq.gz	Fastqsanger.gz
	SRR27968059.fastq.gz	Fastqsanger.gz
	SRR27968060.fastq.gz	Fastqsanger.gz
	SRR27968061.fastq.gz	Fastqsanger.gz

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The integrated stress response finetunes 18S nonfunctional rRNA decay (DMS-MaPseq)

Project description:18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. The underlying mechanisms associated with the detection and turnover of nonfunctional 18S rRNA remain elusive. While NRD has been identified and exclusively studied in Saccharomyces cerevisiae, it is unclear whether this quality control pathway exists in mammals. Here we demonstrate the conservation of 18S NRD in mammalian cells. Using genome-wide CRISPR genetic interaction screens, we identify two molecular events triggered by nonfunctional 18S rRNA— activation of the integrated stress response (ISR) and ubiquitination of ribosomal proteins elicited by GCN2 and RNF10, respectively. Selective ribosome profiling reveals nonfunctional 18S rRNA induces translation arrest at start sites. Biochemical analyses show that activation of the ISR limits translation initiation, attenuating collisions between scanning 43S preinitiation complexes and nonfunctional 80S ribosomes arrested at start sites. Thus, the ISR facilitates the turnover of nonfunctional 18S rRNA and 40S ribosomal proteins by RNF10-mediated ubiquitination. Altogether, these results establish a dynamic feedback mechanism by which cells finetune translation initiation to enable ribosome functionality surveillance through the GCN2-RNF10 axis.

2025-02-26 | GSE255779 | GEO

The integrated stress response finetunes 18S nonfunctional rRNA decay

Project description:The integrated stress response finetunes 18S nonfunctional rRNA decay

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The integrated stress response finetunes 18S nonfunctional rRNA decay (Ribo-Seq)

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The integrated stress response finetunes 18S nonfunctional rRNA decay (SHAP-MaP)

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The integrated stress response finetunes 18S nonfunctional rRNA decay (selective Ribo-Seq)

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The integrated stress response finetunes 18S nonfunctional rRNA decay (SHAP-MaP)

Project description:The integrated stress response finetunes 18S nonfunctional rRNA decay (SHAP-MaP)

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The integrated stress response finetunes 18S nonfunctional rRNA decay (Ribo-Seq)

Project description:The integrated stress response finetunes 18S nonfunctional rRNA decay (Ribo-Seq)

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Probing in vivo RNA structure with optimized DMS-MaPseq in rice

Project description:Here, we use dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to conduct a target-specific and genome-wide profile of in vivo RNA secondary structure in rice (Oryza sativa). Our study presents an optimized DMS-MaPseq for probing in vivo RNA structure in rice.

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The integrated stress response finetunes 18S nonfunctional rRNA decay (selective Ribo-Seq)

Project description:The integrated stress response finetunes 18S nonfunctional rRNA decay (selective Ribo-Seq)

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DMS-MaPseq: A genome-wide or targeted approach for RNA structure probing in vivo

Project description:Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase (TGIRT). DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features for each molecule, and allows genome-wide studies as well as focused investigations of low abundance RNAs. We apply DMS-MaPseq to Drosophila melanogaster ovaries—the first experimental analysis of RNA structure in an animal tissue—and demonstrate its utility in the discovery of a functional RNA structure involved in the non-canonical GUG translation initiation of the human FXR2 mRNA. Additionally, we use DMS-MaPseq to compare the in vivo structure of messages in their pre-mRNA and mature forms. These applications illustrate DMS-MaPseq’s capacity to dramatically expand our ability to monitor RNA structure in vivo.

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