Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA989133 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25071769.fastq.gz	Fastqsanger.gz
	SRR25071770.fastq.gz	Fastqsanger.gz
	SRR25071771.fastq.gz	Fastqsanger.gz
	SRR25071772.fastq.gz	Fastqsanger.gz
	SRR25071773.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

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 [Ribo-seq]

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

| PRJNA989134 | ENA

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

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 down-regulates 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.

| S-EPMC11620358 | biostudies-literature

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:Global alteration of transcript decay rates upon ZNF598 knockdown

| PRJNA975953 | ENA

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.

2024-07-11 | GSE233374 | GEO

HT-SELEX of recombinant C2H2 zinc finger domains of Sall4

2021-01-05 | E-MTAB-9236 | biostudies-arrayexpress

HT-SELEX of recombinant C2H2 zinc finger domains of Sall4

Project description:To define the sequence preference of SALL4 C2H2 zinc finger domains, we performed SELEX coupled with high-throughput sequencing (HT-SELEX) using the purified SALL4 ZFC1, ZFC2 and ZFC4 domains combined with no protein control experiment. We re-sequenced the libraries from E-MTAB-9236 with very high coverage to estimate the minimum number of reads required per sample for accurate results.

2022-03-01 | E-MTAB-11484 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data