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:RNA sequencing for KSHV circular RNAs
| PRJNA498320 | ENA
Project description:Profiling circular RNAs in HeLa cell
| PRJNA490742 | 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
Project description:Circular RNAs (circRNAs), formed by the atypical head-to-tail splicing of exons, have re-emerged as a potentially interesting RNA species given recent reports of a surprising diversity and abundance of circRNA in organisms ranging from worm to human. Here, using deep RNA sequencing, we profiled different RNA species in mouse and observed that circRNAs are significantly enriched in neural tissue, relative to other tissues. Using PacBio sequencing, we determined, for the first time, the circular structure of this population of circRNAs as well as their full-length sequences. We discovered that a disproportionate fraction of the brain circRNA population is derived from host genes that code for synaptic proteins. Moreover, based on the separate profiling of the RNAs localized in neuronal cell bodies and neuropil (enriched in axons and dendrites), we found that, on average, circular RNAs are more enriched in the neuropil than their host gene mRNA isoforms. Using high resolution in situ hybridization we, for the first time, directly visualized circRNA punctae in the dendrites of neurons. The host gene origin and location of the circRNA in neurons suggest the possibility that circRNAs might participate in the regulation of synaptic function and plasticity. Consistent with this idea, we observed via profiling at different developmental stages, that the abundance of many circular RNAs changes abruptly at a time corresponding to synaptogenesis. In addition, following a homeostatic downscaling of neuronal activity many circRNAs exhibit significant up or down-regulation. These data indicate that brain circRNAs are positioned to respond to and regulate synaptic function. Circular RNA profiling in 13 different samples in mice and four samples in rat, using Illumina sequencing
2015-02-25 | E-GEOD-61991 | biostudies-arrayexpress