Robust RNA editing via recruitment of endogenous ADARs using circular guide RNAs
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ABSTRACT:
ORGANISM(S): Mus musculus Homo sapiens
PROVIDER: GSE164956 | GEO | 2021/11/15
REPOSITORIES: GEO
Similar Datasets
Project description:Robust RNA editing via recruitment of endogenous ADARs using circular guide RNAs
| PRJNA692618 | ENA
Project description:Molecular tools to target RNA site‐specifically allow recoding of RNA information and processing. SNAP‐tagged deaminases, guided by a chemically stabilized guideRNA, enable the simultaneous editing of targeted adenosine to inosine in several endogenous transcripts, with high efficiency (up to 90%), high potency, sufficient duration, and high precision. We applied SNAP‐ADARs for the efficient and concurrent editing of two disease‐relevant signaling transcripts, KRAS and STAT1. We also show improved performance compared to the recently described Cas13b-ADAR.
2018-06-01 | GSE112787 | GEO
Project description:Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that convert adenosine to inosine in double-stranded RNA (dsRNA). To evaluate effects of ADARs on small RNAs that derive from dsRNA precursors, we performed deep-sequencing, comparing small RNAs from wildtype and ADAR mutant C. elegans. While editing in small RNAs was rare, at least 40% of microRNAs had altered levels in at least one ADAR mutant strain, and miRNAs with significantly altered levels had mRNA targets with correspondingly affected levels. About 40% of siRNAs derived from endogenous genes (endo-siRNAs) also had altered levels in at least one mutant strain, including 63% of Dicer-dependent endo-siRNAs. The 26G class of endo-siRNAs was significantly affected by ADARs, and many altered 26G loci had intronic reads, and histone modifications associated with transcriptional silencing. Our data indicate ADARs, through both direct and indirect mechanisms, are important for maintaining wildtype levels of many small RNAs in C. elegans. Deep sequencing of small RNAs in wild-type (N2), adr-1 null, adr-2 null and adr-1;adr-2 null mixed stage C. elegans
2012-04-04 | E-GEOD-28888 | biostudies-arrayexpress
Project description:Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that convert adenosine to inosine in double-stranded RNA (dsRNA). To evaluate effects of ADARs on small RNAs that derive from dsRNA precursors, we performed deep-sequencing, comparing small RNAs from wildtype and ADAR mutant C. elegans. While editing in small RNAs was rare, at least 40% of microRNAs had altered levels in at least one ADAR mutant strain, and miRNAs with significantly altered levels had mRNA targets with correspondingly affected levels. About 40% of siRNAs derived from endogenous genes (endo-siRNAs) also had altered levels in at least one mutant strain, including 63% of Dicer-dependent endo-siRNAs. The 26G class of endo-siRNAs was significantly affected by ADARs, and many altered 26G loci had intronic reads, and histone modifications associated with transcriptional silencing. Our data indicate ADARs, through both direct and indirect mechanisms, are important for maintaining wildtype levels of many small RNAs in C. elegans.
2012-04-05 | GSE28888 | GEO
Project description:Here, we reveal that the Caenorhabditis elegans ADAR proteins promote survival of animals exposed to several opportunistic human pathogens. Our data indicate that ADARs help maintain proper levels of cuticular collagen genes, which in turn affects defense of the nematode to these bacteria.
2023-04-01 | GSE223919 | GEO
Project description:Huge efforts are made to engineer safe and efficient genome editing tools. An alternative might be the harnessing of ADAR-mediated RNA editing. We now present the engineering of chemically optimized antisense oligonucleotides that recruit endogenous human ADARs to edit endogenous transcripts in a simple and programmable way, an approach we refer to as RESTORE. Notably, RESTORE was markedly precise, and there was no evidence for perturbation of the natural editing homeostasis. We applied RESTORE to a panel of standard human cell lines, but also to several human primary cells including hepatocytes. In contrast to other RNA and DNA editing strategies, this approach requires only the administration of an oligonucleotide, circumvents the ectopic expression of proteins, and thus represents an attractive platform for drug development. In this respect we have shown the repair of the PiZZ mutation causing α1-antitrypsin deficiency and the editing of phosphotyrosine 701 in STAT1.
2018-12-01 | GSE121573 | GEO
Project description:Cellular RNAs containing double-stranded RNA (dsRNA) structures are subject to A-to-I RNA editing by the adenosine deaminases that act on RNA (ADARs). While A-to-I editing can alter mRNA coding potential, most editing is observed in non-coding sequences, the function of which remains poorly characterized. To correlate small RNA population with expression patterns of ADARs and hyperedited RNAs (editing-enriched regions: EERs) defined and characterized in a separate RNAseq analysis, we re-analyzed existing smallRNAseq datasets of a wildtype strain and a strain lacking ADARs (adr-1;adr-2). Analysis of primary siRNAs from mixed-stage worms revealed that ADARs impact siRNA biogenesis from EERs. We then analyzed primary and secondary RNAs mapping to EERs from embryo-stage or L4-stage worms and observed that ADAR effects on siRNA levels are dependent on developmental stage.
2018-02-23 | GSE89765 | GEO
Project description:Circular RNAs (circRNAs) are produced by head-to-tail back-splicing which is mainly facilitated by base-pairing of reverse complementary matches (RCMs) in circRNA flanking introns. Adenosine deaminases acting on RNA (ADARs) are known to bind double-stranded RNAs for adenosine to inosine (A-to-I) RNA editing. Here we characterize ADARs as potent regulators of circular transcriptome by identifying over a thousand of circRNAs regulated by ADARs in a bidirectional manner through and beyond their editing function. We found that editing can stabilize or destabilize secondary structures formed between RCMs via correcting A:C mismatches to I(G)-C pairs or creating I(G).U wobble pairs, respectively. We provided experimental evidence that editing also favors the binding of RNA-binding proteins such as PTBP1 to regulate back-splicing. These ADARs-regulated circRNAs which are ubiquitously expressed in multiple types of cancers, demonstrate high functional relevance to cancer. Our findings support a hitherto unappreciated bidirectional regulation of circular transcriptome by ADARs and highlights the complexity of cross-talk in RNA processing and its contributions to tumorigenesis.
2022-01-25 | GSE164681 | GEO
Project description:A-to-I RNA editing is widespread in eukaryotic transcriptomes and plays an essential role in the creation of proteomic and phenotypic diversity. Loss of ADARs, the proteins responsible for A-to-I editing, results in lethality in mammals. In C. elegans, knocking out both ADARs, ADR-1 and ADR-2, results in aberrant behavior and abnormal development. Studies have shown that ADR-2 can actively deaminate dsRNA while ADR-1 cannot. However, as most studies of C. elegans ADARs were performed on worms mutated in both ADAR genes, the effects observed cannot be attributed to a single ADAR or to the interactions between ADAR genes. Therefore, we set to study the effects of each C. elegans ADAR on RNA editing, gene expression, protein levels and the contribution of each of ADAR to the phenotypes observed in worms mutated in both genes, in order to elucidate their distinct functions. We found significant differences in the phenotypes observed in worms mutated in a single ADAR gene. Worms harboring adr-1 mutations have a significant reduction in their lifespan, while worms harboring adr-2 mutations have extended lifespan. We also observed severe abnormalities in vulva formation mainly in adr-1 mutants, and we suggest that these phenotypes are a result of an RNA editing independent function of ADR-1. Mutations in each ADAR resulted in expressional changes in hundreds of genes, and a significant downregulation of edited genes. However, very few changes in the protein levels were observed. In addition, we found that ADR-1 binds many edited genes. Our results suggest that ADR-1 has a significant function in the RNA editing process and by altering editing levels it causes the severe phenotypes that we observed. In contrast, a complete lack of RNA editing is less harmful to the worms. Furthermore, our results indicate that the effect of RNA editing on the protein content in the cell is minor and probably the main purpose of these modifications is to antagonize or enhance other gene regulatory mechanisms that act on RNA.
2019-04-22 | GSE110701 | GEO
Project description:Adenosine-to-inosine RNA base editing is a strategy developed to safely manipulate genetic information at the RNA level. Particularly promising for clinical implementation is the use of the ubiquitously expressed endogenous editing enzyme ADAR (adenosine deaminase acting on RNA) with tailored guide RNAs. However, the precision of editing could be compromised by global off-target events that can potentially occur throughout the transcriptome. In this study, we introduce a novel circular CLUSTER guide RNA design that recruits endogenous ADAR in vivo. The goals of the whole transcriptome sequencing experiment were to evaluate the A-to-G RNA editing index and the global editing precision of this novel design. To achieve this, Rett syndrome mice harboring a Mecp2 W104Amber mutation were treated either with a circular CLUSTER guide RNA targeting the mutant Mecp2 transcript or a scrambled and thus non-targeting control guide RNA. Both the targeting and the non-targeting guide RNA were encoded as AAV and delivered via retro-orbital injection of 4x10^12 viral genomes per mouse. The used AAV serotype PHP.eB allows cargo delivery to the mouse brain after systemic administration. Four weeks after injection the thalamus was isolated for NGS analysis. Whole transcriptome sequencing showed that the A-to-G RNA editing index was unaffected by treatment with the targeting guide RNA compared to the scrambled non-targeting control. We were unable to identify any global off-target events, excluding mouse to mouse variability, which suggests a very high precision of our approach on the transcriptome-wide level. Harnessing endogenous ADAR with permanent, AAV-driven CLUSTER guide RNAs in the CNS is an important next step towards the development of novel drug modalities that fight neurological diseases.
2024-06-27 | GSE265898 | GEO