Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA376708 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ribosomal protein (RP) L23 is a negative regulator of cell apoptosis. RPL23 overexpression is associated with abnormal apoptotic resistance in CD34+ cells derived from patients with higher-risk myelodysplastic syndrome (MDS). However, the mechanism underlying RPL23-induced apoptotic resistance in higher-risk MDS patients is poorly understood. Gene microarray analysis between RPL23-knockdown (RPL23-KD) and matched control cells (RPL23-NC) was performed to detail global gene expression profiles and to identify differentially expressed genes and potentially involved pathways associated with RPL23 knockdown.
2017-02-25 | GSE95348 | GEO
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.
2024-06-30 | GSE236310 | GEO
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.
2024-06-30 | GSE236307 | GEO
Project description:3' mRNA-seq of protrusions and cell bodies of nt or LARP6 siRNA transfected MDA-MB231 cells. These data show that Ribosomal protein (RP) -mRNAs localization to cell protrusions is mediated by LARP6.
2022-10-03 | E-MTAB-8472 | biostudies-arrayexpress
Project description:We found ribosomal transcription factor Ifh1p is dynamically acetylated and phosphorylated in response to nutrient cues. ChIP-seq data revealed dynamic binding to ribosomal genes (RP) during the OX growth phase of the yeast metabolic cycle (YMC) when RP genes are highly induced, and weaker binding in the RC quiescent-like phase. Besides RP genes, our ChIP-seq data also reveals binding of Ifh1p to non-RP genes such as translation factors and metabolic genes.
2013-07-05 | GSE39147 | GEO
Project description:3' mRNA-seq of protrusions and cell bodies of a panel of normal and malignant cell lines. These data show that Ribosomal protein (RP) -mRNAs localization to cell protrusions is a conserved phenomenon.
2020-10-30 | E-MTAB-8470 | biostudies-arrayexpress
Project description:We found ribosomal transcription factor Ifh1p is dynamically acetylated and phosphorylated in response to nutrient cues. ChIP-seq data revealed dynamic binding to ribosomal genes (RP) during the OX growth phase of the yeast metabolic cycle (YMC) when RP genes are highly induced, and weaker binding in the RC quiescent-like phase. Besides RP genes, our ChIP-seq data also reveals binding of Ifh1p to non-RP genes such as translation factors and metabolic genes. Examination of Ifh1p binding over two timepoints of the YMC (OX, RC) using Input as the control.
2013-07-05 | E-GEOD-39147 | biostudies-arrayexpress
Project description:We found that CDK11 KD in hESCs caused hESC differentiation. To get the detailed mechanism why its KD caused differentiation, we applied RNA-seq analysis, aiming to find out some clues about the mechanism. Firstly, we obtained the differentially expressed genes (DEGs) from NC and CDK11 KD hESC cells, replicated NC and 2 sets of CDK11 siRNA were transfected into SHhES8 cells for 4 days. Later, we analyzed the data and used GO analysis to enrich GO terms which might be helpful for our research.
2018-12-07 | GSE123410 | GEO
Project description:mRNA Seq analysis of Drosophila wing imaginal discs from Rp mutants and controls in the presence and absence of RpS12 mutations RpS12 is a regulatory gene required for Xrp1-mediated control of translation and growth in mutants for other ribosomal protein genes Loss of function mutations in Ribosomal Protein (Rp) genes are generally lethal, but heterozygous mutant phenotypes increasingly reveal previously cryptic functions of Rps in growth control and tumor suppression. Here we report that RpS12 in particular is a regulatory gene that controls its own expression levels and also signals to control hundreds of gene expression changes in mutants for haploinsufficient Rp genes, acting through the bZip protein Xrp1. Through Xrp1, RpS12 reduces the bulk translation rate of Rp mutant cells and increases the developmental rate of Rp mutant genotypes. RpS12 also has an Xrp1-independent, positive contribution to normal development, so that the effects of RpS12 mutations in different genetic backgrounds reflects the sum of the Xrp1-dependent and Xrp1-independent effects. Our findings outline a regulatory response to mutations affecting essential Rp genes that controls overall translation and growth.
2019-12-17 | GSE124924 | GEO
Project description:We demonstrate that the cell cycle regulators, E2f /Dp and Rb, control the transcription of ribosomal proteins (RP) in Drosophila embryos. Mutation of E2f1 or Dp and over expression of Rbf1 increase and reduce RP transcription, respectively. Although E2f/Dp/Rb might exert this effect through a repressor complex, the regulatory regions of RP genes do not show an enrichment of canonical E2f binding sites. In addition, E2f1, Dp and Rbf1 also regulate the expression of RACK1, a ribosomal component and a negative regulator of cell cycle progression. These findings strengthen the coupling of cell cycle regulation to protein biosynthesis. Keywords: genotype response
2008-04-27 | GSE7655 | GEO