Characterization of group I introns in generating circular RNAs as vaccines [SPLASH]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1162315 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30709220_1.fastq.gz | Fastqsanger.gz | |||
| SRR30709220_2.fastq.gz | Fastqsanger.gz | |||
| SRR30709221_1.fastq.gz | Fastqsanger.gz | |||
| SRR30709221_2.fastq.gz | Fastqsanger.gz | |||
| SRR30709222_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Group 1 introns can be utilized for efficient circularization of RNA molecules. However different group 1 introns are known to have different properties, including having different efficiencies of circularization and generating different levels of immune response inside cells (reactogenicity). Here, we investigated generating circular RNAs using permuted intron-exon (PIE) systems of group 1 introns from different organisms. We observed that group 1 intron sequences have variable circularization efficiency that is size dependent and circularize with high accuracy. We also determined the sequence properties of the exon1 and exon2 domains of different group1 introns and showed that we can engineer elements such as S1 tag into this domain for better purification. Structural probing and mutational analysis in group 1 introns and their PIE RNAs showed that structural features in P2 and P9 domains are correlated with circularization efficiency and that swapping sequences can improve circularization efficiency. Lastly, we showed that circular RNAs made by Sd group 1 introns elicit lower amount of reactogenicity and either An or Sd can act as effective RNA vaccines. Our work deepens the understanding of the properties of group 1 introns and their use in circular RNA production and medicine.
2025-03-12 | GSE239954 | GEO
Project description:Group I introns can be utilized for efficient circularization of RNA molecules; however different introns show variations in their efficiencies of circularization and immune response inside cells. Here, we generated circular RNAs using permuted intron-exon (PIE) systems of group I introns from eight different organisms. We observed that group I introns have variable circularization efficiencies, circularize with high accuracies, and form circular RNAs with distinct reactogenicities. Group I introns also exhibit different sequence requirements for their exon1 and exon2 domains, enabling us to engineer elements such as a S1 tag for better purification. Structural probing and mutational analysis in group I introns and their PIE RNAs showed that structural features in P2 and P9 domains are correlated with circularization efficiency and that swapping sequences can restore pairing to improve circularization. Additionally, RNA modifications do not increase protein production but decrease the reactogenicity of circular RNAs. We demonstrated that circular RNAs made by Scytalidium dimidiatum group I intron elicit strong immunogenicity against SPIKE protein and serve as effective RNA vaccines. Our work deepens the understanding of the properties of group I introns and expands the panel of introns that can be used to generate circular RNAs for vaccines and therapeutics.
2025-03-12 | GSE277434 | GEO
Project description:Characterization of group I introns in generating circular RNAs as vaccines
| PRJNA1001818 | ENA
Project description:Circular RNAs are an increasingly important class of RNA molecules that can be engineered as RNA vaccines and therapeutics. Here, we screened eight different group I introns for their ability to circularize and delineated different features that are important for their function. First, we identified the Scytalidium dimidiatum group I intron as causing minimal innate immune activation inside cells, underscoring its potential to serve as an effective RNA vaccine without triggering unwanted reactogenicity. Additionally, mechanistic RNA structure analysis was used to identify the P9 domain as important for circularization, showing that swapping sequences can restore pairing to improve the circularization of poor circularizers. We also determined the diversity of sequence requirements for the exon 1 and exon 2 (E1 and E2) domains of different group I introns and engineered a S1 tag within the domains for positive purification of circular RNAs. In addition, this flexibility in E1 and E2 enables substitution with less immunostimulatory sequences to enhance protein production. Our work deepens the understanding of the properties of group I introns, expands the panel of introns that can be used, and improves the manufacturing process to generate circular RNAs for vaccines and therapeutics.
| S-EPMC11879131 | biostudies-literature
Project description:In eukaryotic cells, most introns are degraded soon after splicing in the nucleus but some persist either due to lack of splicing (detained/retained introns) or because they contain important functional elements, for example, sno/scaRNAs. Few introns are detectable outside the nucleus. To hunt for interesting new phenomena in cytoplasmic introns and splicing, we conducted a multimodal study of total RNA within projections (axons, dendrites, glial projections) of rat hippocampal neurons and discovered a class of free circular introns enriched in distal projections.
2019-04-18 | GSE129924 | GEO
Project description:Circular RNAs (circRNAs) have gained significant attention in recent years due to their diverse biological functions and potential as novel therapeutic modality. Two general mechanisms for generating circRNAs involves the utilization of group 1 and group 2 introns, which are self-splicing ribozymes found in many organisms. Although group 1 intron has been demonstrated to be highly effective in circularization, the reaction requires high temperature plus cofactors such as GTP. Consequently, undesired byproducts such as nicked RNA were generated, which requires complex purification steps before downstream applications. In this study, we have strategically designed structural elements and incorporated sequence features to enhance the efficacy of RNA circularization by group 2 introns. This innovative approach occurred at a reduced temperature and resulted in notably fewer nicks compared to group 1 introns. Furthermore, to streamline the purification process of circular RNA, we incorporated two halves of streptavidin aptamer tags into the enzymatic sites of the group 2 intron. This strategic architecture guarantees the creation of a fully operational streptavidin aptamer tag solely at the circular RNA junction site during in vitro circularization. This unique attribute facilitates a one-step purification process. The resulting "NicOPURE" system emerges as both straightforward and efficient in generating therapeutic circular mRNAs.
2023-10-29 | GSE246246 | GEO
Project description:Free circular introns with an unusual branchpoint in neuronal projections
| PRJNA533159 | ENA
Project description:We report the discovery of a class of abundant circular noncoding RNAs that are produced during metazoan tRNA splicing. These transcripts, termed tRNA intronic circular (tric)RNAs, are conserved features of animal transcriptomes. Biogenesis of tricRNAs requires anciently conserved tRNA sequence motifs and processing enzymes, and their expression is regulated in an age-dependent and tissue-specific manner. Furthermore, we exploited this biogenesis pathway to develop an in vivo expression system for generating "designer" circular RNAs in human cells. Reporter constructs expressing RNA aptamers such as Spinach and Broccoli can be used to follow the transcription and subcellular localization of tricRNAs in living cells. Owing to the superior stability of circular vs. linear RNA isoforms, this expression system has a wide range of potential applications, from basic research to pharmaceutical science.
| S-EPMC4536317 | biostudies-literature
Project description:Circular DNA tumor viruses make circular RNAs
| PRJNA483204 | ENA
Project description:Natural circular RNAs have been found to sequester microRNAs and suppress their function. We have used this principle as a molecular tool, and produced artificial circular RNA sponges in a cell-free system by in vitro transcription and ligation. Formerly, we were able to inhibit hepatitis C virus propagation by applying a circular RNA decoy strategy against microRNA-122, which is essential for the viral life cycle. In another proof-of-principle study, we used circular RNAs to sequester microRNA-21, an oncogenic and pro-proliferative microRNA. This strategy slowed tumor growth in a 3D cell culture model system, as well as in xenograft mice upon systemic delivery. In the wake of the global use of an in vitro transcribed RNA in Covid-19 vaccines, the question arose if therapeutic circular RNAs trigger cellular antiviral defense mechanisms when delivered systemically. In this study, we present data on the cellular innate immune response as a consequence of liposome-based transfection of the circular RNA sponges we previously used to inhibit microRNA function. We find that circular RNAs produced by the presented methodology do not trigger the antiviral response and do not activate innate immune signaling pathways.
2022-04-08 | GSE192656 | GEO