Effect of DIS3 knockdown on circRNA expression
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ABSTRACT:
PROVIDER: PRJNA1079231 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To investigate the effect of DIS3 KD on circRNA expression in 293T cell line
2025-02-16 | GSE256341 | GEO
Project description:We investigated the effect on miRNA expression in Drosophila melanogaster wing imaginal discs following the knockdown of the 3'-5' exoribonuclease Dis3.
2015-06-01 | E-MTAB-3569 | biostudies-arrayexpress
Project description:To investigate the locolization between DIS3 and circRNA in fractions form sucrose density gradient centrifugation (SDGC) assay for 293T cells
2025-02-16 | GSE256498 | GEO
Project description:The effect of Dis3 knockdown on miRNA expression in Drosophila wing imaginal discs.
| PRJEB9409 | ENA
Project description:Circular RNAs (circRNAs), a noncoding RNA class originating from alternative splicing, are highly abundant in neural tissues and were shown to regulate gene expression e.g. by interacting with microRNAs and RNA-binding proteins. Neuroblastoma is an embryonal neoplasia, which arises from undifferentiated neural crest cells. Here, we aimed to explore, whether circRNAs influence the pathogenesis of high-risk neuroblastoma. We performed whole-transcriptome sequencing of 104 primary neuroblastoma samples of all risk-groups and identified 5,203 unique circRNAs involving 2,302 genes. Candidate circRNA expression did not correlate with host gene expression, indicating independent regulatory mechanisms. circRNAs were significantly downregulated in the MYCN-amplified high-risk tumors. These findings were independently reproduced in a tetracycline-inducible MYCN-overexpression system based on a non MYCN-amplified neuroblastoma cell line, suggesting that MYCN drives this global circRNA repression. We identified the RNA helicase DHX9 as a mediator of this global suppressive effect of MYCN on circRNAs. Comparing our RNA sequencing data with other cancers and controls revealed a circRNA subset specifically upregulated in neuroblastoma that included a circRNA derived from the ARID1A tumor suppressor gene. Specific circARID1A knockdown resulted in reduced proliferation, cell numbers and viability, prompted apoptosis and induced a differentiated phenotype. Neither knockdown, nor overexpression of circARID1A influenced ARID1A mRNA and protein levels significantly. To dissect the potential mode of function, we performed a pulldown assay with subsequent mass spectrometry. We identified the RNA-binding protein KHSRP as an interaction partner that participates in the mechanism of action of circARID1A. In summary, this study highlights an important role of circRNAs in neuroblastoma biology and may establish this RNA class as a future therapeutic target and biomarker.
2023-04-06 | PXD026053 | Pride
Project description:Multiple myeloma (MM) is a plasma cell neoplasm that remains incurable regardless of the introduction of novel agents. Therefore, it is of necessity to decode the molecular mechanisms of myelomagenesis to identify novel therapeutic strategies. Recent advances in next-generation sequencing technologies have not only reconfirmed the significance of known driver events in MM but also have identified novel genetic alterations in MM. Importantly, mutations of DIS3 genes have been identified in ~10% of MM patients, and loss of heterozygosity at chromosome 13q that leads to deletion of one allele of DIS3 has been observed in ~ 40% of MM patients. However, the roles of DIS3 in hematopoiesis and myelomagenesis remain incompletely understood. Here we show that Dis3 prevents accumulation of DNA damage in hematopoietic cells, thereby supporting hematopoiesis. We also show that loss of Dis3 alone and in combination with c-MAF transgene in GC B cells do not exhibit plasma cell neoplasm in mice.
2024-02-28 | GSE244166 | GEO
Project description:Somatic mutations affecting DIS3, the catalytic component of the RNA exosome, have been found in up to 18% of patients affected by the hematological cancer multiple myeloma. Here we show that DIS3 targets and degrades the pluripotency factor LIN28B. In cancer cells, DIS3 inactivation leads to enhanced LIN28B expression, thus disrupting the let-7 miRNAs tumor suppressor network and ultimately increasing protein levels of crucial oncogenes such as MYC and RAS. DIS3 represents the catalytic component of the exosome. The exosome is required for cell viability and targets several RNA species, including pre-mRNAs, pre-tRNAs, pre-rRNAs, snRNAs and snoRNAs. To gain insight on the macular wiring underlying DIS3 activity in mammalian cells, we comprehensively evaluated expression profiles, including miRNAs, in various cell lines, upon DIS3 knockdown.
2015-06-12 | GSE55246 | GEO
Project description:Effect of PM2.5 on circRNA expression of HBE cells
| PRJNA1191831 | ENA
Project description:Somatic mutations affecting DIS3, the catalytic component of the RNA exosome, have been found in up to 18% of patients affected by the hematological cancer multiple myeloma. Here we show that DIS3 targets and degrades the pluripotency factor LIN28B. In cancer cells, DIS3 inactivation leads to enhanced LIN28B expression, thus disrupting the let-7 miRNAs tumor suppressor network and ultimately increasing protein levels of crucial oncogenes such as MYC and RAS. DIS3 represents the catalytic component of the exosome. The exosome is required for cell viability and targets several RNA species, including pre-mRNAs, pre-tRNAs, pre-rRNAs, snRNAs and snoRNAs. To gain insight on the macular wiring underlying DIS3 activity in mammalian cells, we comprehensively evaluated expression profiles, including miRNAs, in various cell lines, upon DIS3 knockdown. This series of microarray experiments contains the miRNA expression profiles of independent replicates of RPMI-8226, KMS12-BM multiple myeloma cell lines and HEK-293T cells, knocked-down with a scrambled or hDIS3 sh4 and collected 72 hours after infection. 500 nanograms of total RNA were processed using the FlashTag labeling kit, which uses a tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample. The labelled RNA was then hybridized to Affymetrix GeneChip® microRNA arrays v1.0, following the Affymetrix manufacturer's instructions.
2015-06-12 | E-GEOD-55246 | biostudies-arrayexpress
Project description:The aim of this study was to investigate the effect of p62 on circRNA and mRNA expression profiles in U-937 cells.
2024-12-31 | GSE220174 | GEO