In vivo RNAi mediated knockdown of translation initiation factor eIF3m is associated with alterations in ribosome biogenesis [RNAseq/Riboseq]
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ABSTRACT:
PROVIDER: PRJNA493293 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7907160.fastq.gz | Fastqsanger.gz | |||
| SRR7907170.fastq.gz | Fastqsanger.gz | |||
| SRR7907161.fastq.gz | Fastqsanger.gz | |||
| SRR7907171_1.fastq.gz | Fastqsanger.gz | |||
| SRR7907171_2.fastq.gz | Fastqsanger.gz |
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Project description:Translation is a fundamental biological process, which defines every aspect of cell physiology. Dysregulation of protein synthesis is associated with the diseases, such as ribosomopathies, diabetes, and cancer. To examine translation dysregulation in vivo, we employed RNA interference to knockdown m-subunit of the translation initiation factor eIF3 exclusively in mouse liver. We observed an increase in the number of monosomes and multiple signs of impaired translation. We further characterized the early cellular response using transcriptome sequencing, ribosome profiling, whole proteome, and phosphoproteome analyses. The major response of hepatocytes to eIF3m deficiency was associated with the changes in mRNA expression, with almost no effect on translation efficiency for particular mRNAs. The transcription changes fell into two main categories: ribosome biogenesis (increased transcription of ribosomal proteins, dephosphorylation of eIF2α, and inhibition of rRNA processing) and cell metabolism (lipid, amino acid, nucleic acid, and drug metabolism). Overall, this work uncovers a new mode of regulation of protein synthesis mediated by the inhibition of translation initiation. It also highlights advantages of RNAi-based in vivo approach for studying regulatory network associated with essential factors involved in mammalian translation.
2020-07-29 | GSE120533 | GEO
Project description:Translation is a fundamental biological process, which defines every aspect of cell physiology. Dysregulation of protein synthesis is associated with the diseases, such as ribosomopathies, diabetes, and cancer. To examine translation dysregulation in vivo, we employed RNA interference to knockdown m-subunit of the translation initiation factor eIF3 exclusively in mouse liver. We observed an increase in the number of monosomes and multiple signs of impaired translation. We further characterized the early cellular response using transcriptome sequencing, ribosome profiling, whole proteome, and phosphoproteome analyses. The major response of hepatocytes to eIF3m deficiency was associated with the changes in mRNA expression, with almost no effect on translation efficiency for particular mRNAs. The transcription changes fell into two main categories: ribosome biogenesis (increased transcription of ribosomal proteins, dephosphorylation of eIF2α, and inhibition of rRNA processing) and cell metabolism (lipid, amino acid, nucleic acid, and drug metabolism). Overall, this work uncovers a new mode of regulation of protein synthesis mediated by the inhibition of translation initiation. It also highlights advantages of RNAi-based in vivo approach for studying regulatory network associated with essential factors involved in mammalian translation.
2020-07-29 | GSE118394 | GEO
Project description:Translation is a fundamental biological process, which defines every aspect of cell physiology. Dysregulation of protein synthesis is associated with the diseases, such as ribosomopathies, diabetes, and cancer. To examine translation dysregulation in vivo, we employed RNA interference to knockdown m-subunit of the translation initiation factor eIF3 exclusively in mouse liver. We observed an increase in the number of monosomes and multiple signs of impaired translation. We further characterized the early cellular response using transcriptome sequencing, ribosome profiling, whole proteome, and phosphoproteome analyses. The major response of hepatocytes to eIF3m deficiency was associated with the changes in mRNA expression, with almost no effect on translation efficiency for particular mRNAs. The transcription changes fell into two main categories: ribosome biogenesis (increased transcription of ribosomal proteins, dephosphorylation of eIF2α, and inhibition of rRNA processing) and cell metabolism (lipid, amino acid, nucleic acid, and drug metabolism). Overall, this work uncovers a new mode of regulation of protein synthesis mediated by the inhibition of translation initiation. It also highlights advantages of RNAi-based in vivo approach for studying regulatory network associated with essential factors involved in mammalian translation.
2020-07-29 | GSE118393 | GEO
Project description:In vivo RNAi mediated knockdown of translation initiation factor eIF3m is associated with alterations in ribosome biogenesis
| PRJNA485434 | ENA
Project description:In vivo RNAi mediated knockdown of translation initiation factor eIF3m is associated with alterations in ribosome biogenesis (rRNA-seq)
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Project description:In vivo RNAi mediated knockdown of translation initiation factor eIF3m is associated with alterations in ribosome biogenesis (mRNA-seq)
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Project description:Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat-stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3’ end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3’ end maturation or metabolism. We quantitatively defined new processing hotspots and identified adenylation as the prevalent non-templated RNA modification at the 3’ ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNAi to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3’ portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late-40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, mRNA translation initiation, and siRNA biogenesis in plants.
2023-04-19 | GSE223171 | GEO
Project description:Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat-stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3’ end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3’ end maturation or metabolism. We quantitatively defined new processing hotspots and identified adenylation as the prevalent non-templated RNA modification at the 3’ ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNAi to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3’ portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late-40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, mRNA translation initiation, and siRNA biogenesis in plants.
2023-04-19 | GSE223169 | GEO
Project description:Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat-stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3’ end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3’ end maturation or metabolism. We quantitatively defined new processing hotspots and identified adenylation as the prevalent non-templated RNA modification at the 3’ ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNAi to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3’ portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late-40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, mRNA translation initiation, and siRNA biogenesis in plants.
2023-04-19 | GSE223168 | GEO
Project description:Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat-stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3’ end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3’ end maturation or metabolism. We quantitatively defined new processing hotspots and identified adenylation as the prevalent non-templated RNA modification at the 3’ ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNAi to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3’ portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late-40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, mRNA translation initiation, and siRNA biogenesis in plants.
2023-04-19 | GSE223167 | GEO