Mus musculus
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR087002.fastq.gz | Fastqsanger.gz | |||
| DRR087003.fastq.gz | Fastqsanger.gz | |||
| DRR087004.fastq.gz | Fastqsanger.gz | |||
| DRR087005.fastq.gz | Fastqsanger.gz | |||
| DRR087006.fastq.gz | Fastqsanger.gz |
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Project description:RNAseq analysis of cell lines with ADAR1-p150 and ADAR1-p110 knock-outs and primary human tissue samples (from GSE57353 and GSE99392 data sets) to identify sites of ADAR1 editing
2018-12-04 | GSE115127 | GEO
Project description:Adenosine deaminase acting on RNA (ADAR) (also known as ADAR1) promotes A-to-I conversion in double-stranded and highly structured RNAs. ADAR1 has two isoforms transcribed from different promoters: ADAR1p150, which is mainly cytoplasmic and interferon-inducible, and constitutively expressed ADAR1p110 that is primarily localized in the nucleus. Mutations in ADAR1 cause Aicardi – Goutières syndrome (AGS), a severe autoinflammatory disease in humans associated with aberrant IFN production. In mice, deletion of ADAR1 or selective knockout of the p150 isoform alone leads to embryonic lethality driven by overexpression of interferon-stimulated genes. This phenotype can be rescued by concurrent deletion of cytoplasmic dsRNA-sensor MDA5. These findings indicate that the interferon-inducible p150 isoform is indispensable and cannot be rescued by the ADAR1p110 isoform. Nevertheless, editing sites uniquely targeted by ADAR1p150 but also mechanisms of isoform- specificity remain elusive. To identify ADAR1 isoform-specific ‘editome’, we transfected A-to-I editing deficient mouse embryonic fibroblasts (MEFs) with ADAR1p150- or ADAR1p110- or RFP-editing negative control. We subjected the samples to RNA sequencing and detected editing at known-editing sites.
2021-11-17 | GSE188842 | GEO
Project description:RNA editing by adenosine deaminases acting on RNA (ADARs) is an evolutionarily conserved posttranscriptional modification essential for organismal development and normal cell function. Three catalytically active ADARs are conserved in mammals: two isoforms of ADAR1 referred to as ADAR1-p150 and ADAR1-p110, as well as ADAR2. All recognize and edit double-stranded RNA (dsRNA) structures but demonstrate target specificity and selectivity that dictate the unique essential biological functions of the three enzymes. The editing activity of ADAR1-p150 suppresses autoimmune responses against self-RNA structures, whereas ADAR1-p110 and ADAR2 have other primary functions. To better understand the mechanism of target selection by ADARs, we developed TSniffer, which allows accurate de novo identification of edited transcripts and quantification of the extent of editing within each transcript. We found that 17-40% of protein coding transcripts in mice, ferrets, and humans are edited by ADARs. Individual transcripts can harbor hundreds and thousands of editing sites, mostly within inverted retrotransposable elements. For human transcripts, we found differential editing by ADAR1 and ADAR2, aligning with a supportive role for ADAR2, while some targets were dominantly edited by ADAR1. Relying only on RNA-seq data and reference genome, TSniffer represents a novel tool to decipher the role of ADAR editing in different physiological states including disease models. Its unbiased approach is suitable for any organism.
2025-12-03 | GSE291676 | GEO
Project description:RNA editing by adenosine deaminases acting on RNA (ADARs) is an evolutionarily conserved posttranscriptional modification essential for organismal development and normal cell function. Three catalytically active ADARs are conserved in mammals: two isoforms of ADAR1 referred to as ADAR1-p150 and ADAR1-p110, as well as ADAR2. All recognize and edit double-stranded RNA (dsRNA) structures but demonstrate target specificity and selectivity that dictate the unique essential biological functions of the three enzymes. The editing activity of ADAR1-p150 suppresses autoimmune responses against self-RNA structures, whereas ADAR1-p110 and ADAR2 have other primary functions. To better understand the mechanism of target selection by ADARs, we developed TSniffer, which allows accurate de novo identification of edited transcripts and quantification of the extent of editing within each transcript. We found that 17-40% of protein coding transcripts in mice, ferrets, and humans are edited by ADARs. Individual transcripts can harbor hundreds and thousands of editing sites, mostly within inverted retrotransposable elements. For human transcripts, we found differential editing by ADAR1 and ADAR2, aligning with a supportive role for ADAR2, while some targets were dominantly edited by ADAR1. Relying only on RNA-seq data and reference genome, TSniffer represents a novel tool to decipher the role of ADAR editing in different physiological states including disease models. Its unbiased approach is suitable for any organism.
2025-12-03 | GSE291675 | GEO
Project description:Cancer immunotherapy efficacy is often limited by primary and acquired resistance. The RNA- editing enzyme ADAR1 has emerged as a key regulator of tumor immune evasion, yet therapeutic targeting is challenged by the essential physiological roles of its constitutively expressed p110 isoform. Here, we identify the interferon-inducible p150 isoform and its Zα domain as a critical therapeutic vulnerability. We demonstrate that ADAR1 p150 is frequently overexpressed in human cancers and correlates with an immunosuppressive tumor microenvironment. Genetic ablation of ADAR1 p150 intrinsically inhibits tumor proliferation and extrinsically triggers a robust type I interferon response and profound remodeling of the tumor immune landscape, converting immunologically "cold" tumors to "hot." Furthermore, we establish that myeloid-specific ADAR1 deletion synergizes with anti-PD-1 therapy by enhancing antigen presentation and fostering a pro-inflammatory microenvironment. Crucially, we delineate the Zα domain as the essential structural determinant for dsRNA editing selectivity. Targeted disruption of this domain alone, without affecting the catalytic deaminase domain, is sufficient to recapitulate the potent antitumor effects of complete ADAR1 ablation, leading to accumulation of immunogenic dsRNA, activation of cytosolic sensors (MDA5/PKR), and potent anti-tumor immunity. Our work provides a compelling rationale for selectively targeting the ADAR1 p150-Zα axis to reverse malignant RNA editing and overcome resistance to immunotherapy, offering a refined strategy with a potentially superior therapeutic index.
2026-04-12 | GSE316054 | GEO
Project description:Cancer immunotherapy efficacy is often limited by primary and acquired resistance. The RNA-editing enzyme ADAR1 has emerged as a key regulator of tumor immune evasion, yet therapeutic targeting is challenged by the essential physiological roles of its constitutively expressed p110 isoform. Here, we identify the interferon-inducible p150 isoform and its Zα domain as a precise therapeutic vulnerability. We demonstrate that ADAR1 p150 is frequently overexpressed in human cancers and correlates with an immunosuppressive tumor microenvironment. Genetic ablation of ADAR1 p150 intrinsically inhibits tumor proliferation and extrinsically triggers a robust type I interferon response and profound remodeling of the tumor immune landscape, converting immunologically "cold" tumors to "hot." Furthermore, we establish that myeloid-specific ADAR1 deletion synergizes with anti-PD-1 therapy by enhancing antigen presentation and fostering a pro-inflammatory microenvironment. Crucially, we delineate the Zα domain as the essential structural determinant for dsRNA editing fidelity. Targeted disruption of this domain alone, without affecting the catalytic deaminase domain, is sufficient to recapitulate the potent antitumor effects of complete ADAR1 ablation, leading to accumulation of immunogenic dsRNA, activation of cytosolic sensors (MDA5/PKR), and potent anti-tumor immunity. Our work provides a compelling preclinical rationale for selectively targeting the ADAR1 p150-Zα axis to reverse malignant RNA editing and overcome resistance to immunotherapy, offering a refined strategy with a potentially superior therapeutic index.
2026-04-12 | GSE314521 | GEO
Project description:Adenosine-to-inosine (A-to-I) RNA editing mediated by endogenous ADAR enzymes represents a promising therapeutic strategy for correcting disease-causing mutations at the transcript level without permanent genomic modification. To improve endogenous ADAR1 recruitment and RNA editing efficiency, we developed MARRS (Multivalent ADAR1 Recruiting RNA-editing System), a programmable RNA editing platform that incorporates engineered multivalent RNA aptamers targeting the Zα domain of ADAR1 p150 within a circular RNA scaffold. RNA sequencing was performed to characterize transcriptome-wide gene expression changes associated with MARRS and CLUSTER systems compared with control samples. The dataset consists of three experimental groups (Control, CLUSTER, and MARRS), each represented by three biological replicates. These data provide a resource for investigating the molecular consequences of enhanced endogenous ADAR1 recruitment and evaluating the transcriptomic impact of programmable RNA editing strategies.
2026-07-31 | GSE334805 | GEO
Project description:This study aims to delineate the role of ADAR1 in human cells beyond its canonical function as an interferon-stimulated gene (ISG). Human monocyte-derived macrophages were subjected to RNA interference targeting either pan-ADAR1 (both isoforms) or the p150 isoform specifically. Quantitative proteomic analyses were performed using state-of-the-art isobaric tandem mass tag (TMT) labeling coupled with liquid chromatography–tandem mass spectrometry (LC-MS/MS). Strikingly, silencing of ADAR1 significantly impacted prototypical macrophage functions, including endocytosis, cholesterol metabolism, and lysosomal processing, without concurrent induction of pro-inflammatory or ISG responses. Pan-ADAR1 silencing resulted in upregulation of proteins involved in lysosomal function and cholesterol processing, whereas selective depletion of ADAR1-p150 led to downregulation of pathways associated with phagocytosis and endocytosis. Moreover, loss of pan-ADAR1 caused a marked downregulation of cell-cycle and p53 signaling pathways, suggesting a potential role for the ADAR1-p110 isoform in regulating cell proliferation. Collectively, these data define previously unappreciated proteomic alterations driven by ADAR1 that influence fundamental macrophage functions beyond its established ISG role.
2026-02-13 | PXD073582 | Pride
Project description:Adenosine deaminase acting on RNA 1 (ADAR1), is an enzyme that catalyzes the conversion of adenosine to inosine in double-stranded RNA, a process critical for regulation of innate immune response and distinguishing between ‘self and non-self RNA’. It is expressed as two isoforms: nucleolar p110 and cytoplasmic, interferon (IFN)-inducible, p150. The interactome of the p110 under steady-state conditions is well-studied; however, less is known about the interactions of the p150 isoform, particularly during IFN response. To elucidate ADAR1's protein interactions during IFN stimulation, alongside steady-state conditions, three distinct methods of enrichment were used followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). These included: immunoprecipitation (IP) of endogenous ADAR1, IP of Strep II-tagged ADAR1, and proximity labeling using BioID. Individual ADAR1 isoforms (p110 and p150) and their respective dsRNA binding-deficient mutants were created to discern isoform-specific and dsRNA-dependent interactions. Altogether, our results reveal a comprehensive ADAR1 interaction map, identifying both known and novel partners, and highlighting the isoform-specific and dsRNA-binding-dependent nature of ADAR1 interactions. Under IFN stimulation, ADAR1's interaction spectrum encompasses viral replication inhibitors and LINE-1 regulators. Mimicking viral infection with HMW poly(I:C) changed the proximal network of proteins for both isoforms. Our findings provide new insights into ADAR1's roles and its dynamic during IFN response.
2024-12-05 | PXD049681 | Pride
Project description:Adenosine deaminase acting on RNA 1 (ADAR1), is an enzyme that catalyzes the conversion of adenosine to inosine in double-stranded RNA, a process critical for regulation of innate immune response and distinguishing between ‘self and non-self RNA’. It is expressed as two isoforms: nucleolar p110 and cytoplasmic, interferon (IFN)-inducible, p150. The interactome of the p110 under steady-state conditions is well-studied; however, less is known about the interactions of the p150 isoform, particularly during IFN response. To elucidate ADAR1's protein interactions during IFN stimulation, alongside steady-state conditions, three distinct methods of enrichment were used followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). These included: immunoprecipitation (IP) of endogenous ADAR1, IP of Strep II-tagged ADAR1, and proximity labeling using BioID. Individual ADAR1 isoforms (p110 and p150) and their respective dsRNA binding-deficient mutants were created to discern isoform-specific and dsRNA-dependent interactions. Altogether, our results reveal a comprehensive ADAR1 interaction map, identifying both known and novel partners, and highlighting the isoform-specific and dsRNA-binding-dependent nature of ADAR1 interactions. Under IFN stimulation, ADAR1's interaction spectrum encompasses viral replication inhibitors and LINE-1 regulators. Mimicking viral infection with HMW poly(I:C) changed the proximal network of proteins for both isoforms. Our findings provide new insights into ADAR1's roles and its dynamic during IFN response.
2024-12-05 | PXD049689 | Pride