Regulation of highly expressed hCINAP on translatome
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE81469 | GEO | 2016/07/18
SECONDARY ACCESSION(S): PRJNA321727
REPOSITORIES: GEO
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Project description:hCINAP is essential for human 18S rRNA processing and ribosome assembly. hCINAP is highly expressed in human cancers and promotes cancer cell growth. To connect the role of hCINAP in ribosome biogenesis and tumor growth, genome-wide polysome profiling was performed to detect the regulation of hCINAP on ribosome assembly and translation control. The results showed taht hihgly expressed hCINAP promotes ribosome biogenesis and selectively modulates cancer-associated translatome to promote malignancy. This result provides important insights into the molecular mechanism underlying the role of hCINAP in tumorigenesis. For the transcriptional profile, MCF7 cells transfected with control vector or GFP-hCINAP were collected and total RNA was extracted. For the polysoem profile, MCF7 cells with stably expressed GFP or GFP-hCINAP were subjected to surcose gradient fractionation. Ribosome profiles were obtained by measuring the absorbance of the sucrose gradient at a wavelength of 254 nm using a BioComp Gradient Fractionator. The fractions corresponding to subpolysome and polysome were collected and RNA was extracted. The cDNA library was generated and sequenced via Illumina HiSeqTM 2000. The clean reads were mapped to the UCSC hg19 reference genome and FPKM was assigned to calculate expression levels. The recruitment to polysome of each mRNA was calculated according to their FPKM values in the monsome and polysome.
2016-07-18 | E-GEOD-81469 | biostudies-arrayexpress
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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: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: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:Counterintuitively, increased tumour predisposition is associated with ribosomal protein (RP) loss. Here, we provide the first evidence that RP depletion can directly drive tissue overgrowth. Haematopoietic compartment-specific knockdown (KD) of RpS19a in the Drosophila lymph gland not only results in haematopoietic stem and progenitor cell (HSPC) loss but also drives excess proliferation and tissue overgrowth. In accordance with continued ribosome assembly and protein synthesis, actively translating ribosomes (polysomes) are detected in RpS19a KD Drosophila S2 cells. The RpS19a KD ribosomes do, however, display heterogeneity and significantly altered stoichiometry of the associated translation initiation factors eIF4A and eIF5. Consistent with altered translation, in addition to increased association between polysomes and mRNA encoding growth promoting genes (e.g. Ras), we observe increased abundance of the ortholog of ribosomal (r)RNA small subunit methyltransferase NEP1. Although uncharacterised in Drosophila, in yeast and human NEP1 is implicated in methylation of 18S rRNA and, thus, 40S assembly and 80S ribosome stability. Moreover, NEP1 (EMG1) mutations in humans underpin Bowen-Conradi syndrome, a ribosomopathy associated with developmental defects, growth failure, and infantile death. Remarkably, NEP1 depletion suppresses the RpS19a KD phenotype, restoring both stem and progenitor cells and suppressing lymph gland overgrowth. We further demonstrate NEP1 depletion significantly decreases methylation of the 18S rRNA residue (Ψ1,279) that is implicated in ribosome assembly. Together, these data suggest the increased NEP1 expression associated with RpS19a KD promotes assembly of pro-proliferative “onco-ribosomes” to drive haematopoietic compartment overgrowth.
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