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Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish [Ribo-seq]

ABSTRACT: Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish [Ribo-seq]

PROVIDER: PRJNA989134 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25071781.fastq.gz	Fastqsanger.gz
	SRR25071782.fastq.gz	Fastqsanger.gz
	SRR25071783.fastq.gz	Fastqsanger.gz
	SRR25071784.fastq.gz	Fastqsanger.gz

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Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish [Ribo-seq]

Project description:Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision, which is monitored by multiple sensor mechanisms in eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes, triggering ribosome-associated quality control (RQC) to rescue stalled ribosomes and no-go decay (NGD) to degrade stall-prone mRNAs. However, the impact of RQC and NGD on maintaining the translational homeostasis of endogenous mRNAs has remained unclear. In this study, we investigated the endogenous substrate mRNAs of NGD during the maternal-to-zygotic transition (MZT) of zebrafish development. RNA-Seq analysis of zebrafish znf598 mutant embryos revealed that Znf598 downregulates mRNAs encoding the C2H2-type zinc finger domain (C2H2-ZF) during the MZT. Reporter assays and disome profiling indicated that ribosomes stall and collide while translating tandem C2H2-ZFs, leading to mRNA degradation by Znf598. Our results suggest that NGD maintains the quality of the translatome by mitigating the risk of ribosome collision at the abundantly present C2H2-ZF sequences in the vertebrate genome.

2024-10-03 | GSE236144 | GEO

Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish [RNA-seq]

2024-10-03 | GSE236143 | GEO

Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish

Project description:Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish

| PRJNA989127 | ENA

Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish [RNA-seq]

Project description:Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish [RNA-seq]

| PRJNA989133 | ENA

Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-10-03 | GSE236146 | GEO

Global alteration of transcript decay rates upon ZNF598 knockdown

Project description:We calculated half-life of transcripts in HEK293T cells expressing control or ZNF598-targeting shRNA.

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Multiparameter functional diversity of human C2H2 zinc finger proteins [RNA-Seq]

Project description:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2 arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. We have determined the binding sites and motifs of 119 C2H2 zinc finger proteins and the expression pattern of 80 cell lines overexpressing C2H2 zinc finger proteins in order to study the role of C2H2 zinc finger proteins in gene regulation. We expressed GFP-tagged C2H2-ZF proteins in stable transgenic HEK293 cells. Total RNA was isolated using Trizol and sequencing libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold or TruSeq RNA Library Preparation Kit v2.

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