RNA helicase DDX10 is Required for Pluripotency of Stem Cells by Regulating 18S rRNA Processing (CLIP-Seq)
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ABSTRACT:
PROVIDER: PRJNA970812 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24488163.fastq.gz | Fastqsanger.gz | |||
| SRR24488164.fastq.gz | Fastqsanger.gz |
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Project description:Ribosomes, as a protein synthesis machine, are required for stem cells to maintain self-renewal. Here, we find that DEAD-box RNA helicase DDX10 is necessary for cellular pluripotency acquisition in somatic cell reprogramming, and in mouse embryonic stem cells (mESCs), DDX10 degradation disrupts cellular homeostasis, leads to cell cycle arrest in G1 phase and markedly inhibits cell proliferation. DDX10 is localized in dense fiber component (DFC) and granular component (GC), mainly binds to 45S ribosomal RNA (rRNA) and participates in regulating ribosome biogenesis. Specifically, DDX10 degradation prevents the release of U3 snoRNA from pre-rRNA, and disrupts pre-rRNA processing and maturation of 18S rRNA, leading to impaired ribosomal small subunit production. Together, this study reveals that DDX10 functions as an important regulator of ribosome biogenesis, and is essential for the survival, induction and maintenance of pluripotent stem cells.
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Project description:Ribosomes, as a protein synthesis machine, are required for stem cells to maintain self-renewal. Here, we find that DEAD-box RNA helicase DDX10 is necessary for cellular pluripotency acquisition in somatic cell reprogramming, and in mouse embryonic stem cells (mESCs), DDX10 degradation disrupts cellular homeostasis, leads to cell cycle arrest in G1 phase and markedly inhibits cell proliferation. DDX10 is localized in dense fiber component (DFC) and granular component (GC), mainly binds to 45S ribosomal RNA (rRNA) and participates in regulating ribosome biogenesis. Specifically, DDX10 degradation prevents the release of U3 snoRNA from pre-rRNA, and disrupts pre-rRNA processing and maturation of 18S rRNA, leading to impaired ribosomal small subunit production. Together, this study reveals that DDX10 functions as an important regulator of ribosome biogenesis, and is essential for the survival, induction and maintenance of pluripotent stem cells.
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Project description:RNA helicase DDX10 is Required for Pluripotency of Stem Cells by Regulating 18S rRNA Processing
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Project description:SIRT7 is an NAD+-dependent protein deacetylase with important roles in ribosome biogenesis and cell proliferation. Previous studies have established that SIRT7 is associated with RNA polymerase I, interacts with pre-rRNA and promotes rRNA synthesis. Here we show that SIRT7 is also associated with snoRNAs that are involved in pre-rRNA processing and rRNA maturation. Knockdown of SIRT7 impairs U3 snoRNA-dependent early cleavage steps that are necessary for generation of 18S rRNA. Mechanistically, SIRT7 deacetylates U3-55k, a core component of the U3 snoRNP complex, and reversible acetylation of U3-55k modulates the association of U3-55k with U3 snoRNA. Deacetylation by SIRT7 enhances U3-55k binding to U3 snoRNA, which is a prerequisite for pre-rRNA processing. Under stress conditions, SIRT7 is released from nucleoli, leading to hyperacetylation of U3-55k and attenuation of prerRNA processing. The results reveal a multifaceted role of SIRT7 in ribosome biogenesis, regulating both transcription and processing of rRNA. CLIP-seq was performed in Flag-SIRT7-293T cells.
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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.
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Project description:RNA helicase DDX10 is Required for Pluripotency of Stem Cells by Regulating 18S rRNA Processing (RNA-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.
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