Circular RNAs affect mRNA stability
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ABSTRACT:
PROVIDER: PRJNA1002274 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below.
2024-11-28 | GSE240092 | GEO
Project description:Circular RNAs (circRNAs) are a unique class of single-stranded RNA molecules with a closed-loop structure that confer enhanced stability, extended protein expression, and resistance to exonucleases, making them promising candidates for RNA therapeutics. In recent years, several methods have been developed to generate circRNAs, including the traditional, scar-containing Anabaena Permuted Intron-Exon (Ana-PIE) method and newer “scarless” circularization approaches. This study introduces a novel scarless circularization method, Split-Coxsackievirus B3-Anabaena Permuted Intron-Exon (Split-CVB3 Ana-PIE, SCAP). Scarless circular RNAs generated using the SCAP system were systematically compared to their scarred counterparts produced by the Ana-PIE system in terms of circularization efficiency, protein expression, stability, and immune response. The SCAP system achieved circularization efficiencies comparable to those of the Ana-PIE system while significantly enhancing protein expression. Scarless circular RNAs exhibited similar stability to scarred circular RNAs and did not trigger significant immune responses. These findings highlight the potential of scarless circular RNAs in gene therapy and vaccine development, demonstrating that removing extraneous sequences improves translation efficiency without compromising stability or immunogenicity. This study provides a foundation for the rational design of circular RNAs, with future efforts focusing on diverse target genes, optimized delivery platforms, and in vivo validation.
2025-03-01 | GSE284757 | GEO
Project description:Circular DNA tumor viruses make circular RNAs
| PRJNA483204 | ENA
Project description:Purpose: We are using the illumina sequencing to compare the false positive and true positive circular RNA findings to confine the method to detect the true circular RNAs Methods: The testis whole transcriptome profiling was generated from 4-week mouse testis using illumina Nextseq, duplicated. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: our data suggest that circular RNAs identified based on junction sequences in the RNA-seq reads, especially those from Illumina Hiseq sequencing, mostly result from template-switching events during reverse transcription by MMLV-derived reverse transcriptases. It is critical to employ reverse transcriptases lacking terminal transferase activity (e.g., MonsterScript) to construct sequencing library or perform RT-PCR for identification and quantification of true circular RNAs. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. The wild type mouse testis RNAs were constructed NGS library by two different enzyme, then parallel sequenced in illumina Nextseq
2016-07-05 | E-GEOD-83992 | biostudies-arrayexpress
Project description:We performed Ribosome-protected mRNA fragment sequencing (Ribo-Seq) to determine if retinal circular RNAs are undergoing translation
2022-02-14 | GSE166919 | GEO
Project description:Noncoding RNAs play important roles in various biological processes and diseases, including cancer. Expression profile of circular RNAs (circRNA) is largely unknown in lung adenocarcinoma. This study is designed to explore mRNA, long noncoding RNA (lncRNA), and circRNA in lung adenocarcinoma.
2017-10-13 | GSE104854 | GEO
Project description:Circular RNAs (circRNAs) are frequently generated during splicing. Their physiological roles, however, remain largely elusive. Some specific circRNAs function as microRNA (miRNA) or RNA binding protein (RBP) sponges or encode for proteins and are actively translated. Due to the lack of accessible ends, circRNAs are resistant to exonucleolytic cleavage and thus are more stable than linear RNAs. Nevertheless, circRNAs are most likely turned over by cellular degradation pathways. Here, we used a biochemical purification strategy to find nucleases that could degrade circRNAs. We identified the exosome-associated nuclease DIS3, which contains an endonucleolytic PIN domain and an exonuclease domain. We show that DIS3 can degrade circRNAs independently of the exosome in vitro. Although moderately, RNA-seq reveals that selected circRNAs are stabilized when DIS3 is reduced in vivo. Based on our data, we propose a model, in which cytoplasmic DIS3 contributes to the turnover of circRNAs in human cells.
2025-05-05 | PXD050442 | Pride
Project description:Profiling circular RNAs in HeLa cell
| PRJNA490742 | ENA
Project description:RNA sequencing for KSHV circular RNAs
| PRJNA498320 | ENA
Project description:We used RNA-seq to examine circular RNAs from RNase R treated ribo-zero RNAs in HeLa cells.
2019-09-13 | GSE119938 | GEO