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MRNA profiling after knockdown of Circular RNA-INSR

ABSTRACT: mRNA profiling after knockdown of Circular RNA-INSR

PROVIDER: PRJNA818305 | ENA |

REPOSITORIES: ENA

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mRNA profiling after knockdown of Circular RNA-INSR

Project description:The recent advances in anti-cancer treatments have led to a steady increase in the number of cancer survivors, paradoxically also enhancing the number of HF patients who suffer from the undesired cardiotoxic side effects of these anti-tumor treatments. Therapeutic options to reduce or reverse chemotherapy-induced HF are not available. Circular RNAs exhibit high druggability due to the high stability of their special closed loop structure. Circ-INSR overexpression prevents doxorubicin-induced cardiac dysfunction in preclinical murine and human models. Circ-INSR mimics produced in vitro also reduced cardiomyocyte death under doxorubicin stress, highlighting the potential of Circ-INSR-based RNA therapy for future clinical applications.

2022-10-01 | GSE199081 | GEO

mRNA profiling after knockdown of lncRNA Cyrano

Project description:mRNA profiling after knockdown of lncRNA Cyrano

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A Mammalian Conserved Circular RNA CircLARP2 Regulates Hepatocellular Carcinoma Metastasis and Lipid Metabolism (Part 2)

Project description:Circular RNAs (circRNAs) have emerged as crucial regulators in physiology and human diseases. However, evolutionarily conserved circRNAs with potent functions in cancers are rarely reported. Here, we identified a mammalian conserved circRNA circLARP2 that played critical roles in hepatocellular carcinoma (HCC). With clinical specimens, we found that patients with high circLARP2 levels in HCC had advanced prognostic stage and poor overall survival. CircLARP2 facilitated HCC metastasis and lipid accumulation in HCC cell lines. CircLARP2 was one of the rare ones that were identified in HCC metastasis and conserved in mammals, which enabled further studies with animal models. CircLARP2-deficient mice exhibited reduced metastasis and less lipid accumulation in an induced HCC model. We provided lines of evidence at molecular, cellular, and whole organismal levels, to support that circLARP2 functioned as a protein sponge of AUF1. CircLARP2 sequestered AUF1 from binding to LKB1 mRNA, which led to decreased LKB1 mRNA stability and lower LKB1 protein levels. LKB1 as a kinase promoted the phosphorylation of AMPK and then the phosphorylation of ACC, the rate limiting enzyme of fatty acid synthesis. Knockdown of Lkb1 with AAV8-shLkb1 in mice HCC model also proved that Lkb1 was a key element in the regulation. Through this AUF1-LKB1-AMPK-ACC pathway, circLARP2 promoted HCC metastasis and lipid accumulation.

2023-03-10 | ST002395 | MetabolomicsWorkbench

circular Neurexin3 knockdown in rat orbitofrontal cortex

Project description:circular Neurexin3 knockdown in rat orbitofrontal cortex

| PRJNA933181 | ENA

Circular RNA circRERE2 knockdown in rat primary cortical neurons

Project description:Circular RNA circRERE2 knockdown in rat primary cortical neurons

| PRJNA1088105 | ENA

circular Neurexin3 knockdown in rat orbitofrontal cortex

Project description:We report mRNAs differentially expressed in the orbitofrontal cortex of adult male rats 7 days following knockdown of circular Neurexin 3 in the orbitofrontal cortex.

2024-02-09 | GSE224957 | GEO

RNA-mediated activity-based protein profiling reveals dihydrouridine modification on human mRNA

Project description:Epitranscriptomic RNA modifications can regulate RNA activity, however there remains a major gap in our understanding of the scope of mRNA chemistry present in biological systems. Here, we develop RNA-mediated activity-based protein profiling (RNABPP), a chemoproteomic strategy relying upon metabolic RNA labeling with the mechanism-based inhibitor 5-fluorocytidine, mRNA interactome capture, and quantitative proteomics, to investigate pyrimidine-modifying enzymes in human cells. In addition to profiling 5-methylcytidine (m5C) methyltransferase activity on mRNA, metabolic deamination of 5-fluorocytidine to 5-fluorouridine allowed us to show that 5-methyluridine (m5U) is present on human mRNA and demonstrate that its formation is primarily mediated by the tRNA-modifying enzyme TRMT2A. Further, our approach uncovered DUS3L, the mammalian homolog of the yeast tRNA-dihydrouridine synthase DUS3, as a novel 5-fluoropyrimidine-reactive protein. We investigate the mechanism of protein-RNA crosslinking, which involves the conserved catalytic Cys residue, and use genetic knockdown combined with quantitative LC-MS/MS analysis to establish that DUS3L installs dihydrouridine (DHU) on human mRNA and small RNA. Finally, we find that DUS3L is important for cell proliferation and protein translation. Taken together, our work provides a general approach for profiling RNA modifying enzyme activity in vivo, and reveals the existence of new pathways for the epitranscriptomic regulation of mRNA behavior in human cells.

2021-07-16 | PXD022645 | Pride

mRNA and miRNA expression profiling of CUL4B knockdown in MKN45 cells

Project description:mRNA and miRNA expression profiling of CUL4B knockdown in MKN45 cells

| PRJNA354914 | ENA

Circular RNA circRERE2 knockdown in rat primary cortical neurons [polyA RNA-seq]

Project description:Circular RNA circRERE2 knockdown in rat primary cortical neurons [polyA RNA-seq]

| PRJNA1088101 | ENA

Circular RNA circRERE2 knockdown in rat primary cortical neurons [miRNA-seq]

Project description:Circular RNA circRERE2 knockdown in rat primary cortical neurons [miRNA-seq]

| PRJNA1088107 | ENA