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The landscape of A-to-I RNA editome in mouse embryonic development

ABSTRACT: A-to-I editing, as a post-transcriptional modification process mediated by ADAR, plays a crucial role in many biological process in metazoans.The study of RNA editing in mouse early embryonic development can understand the dynamic changes of RNA editing during mouse early embryonic development, and further reveal the role of RNA editing in mouse early embryo development.We found that as embryonic developing, RNA editome in mice is getting more and more. Besides, RNA editome in mouse embryonic development is stage specified.

ORGANISM(S): Mus musculus

PROVIDER: GSE123012 | GEO | 2018/11/28

REPOSITORIES: GEO

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Placental Editome Profiling Reveals Widespread RNA-Editing Dysregulation in Preeclampsia

Project description:Dysregulated RNA editing is well documented in several diseases such as cancer. The extent to which RNA editing might be involved in diseases originated in the placenta such as preeclampsia remains unknown, because RNA editing has rarely been studied in the placenta. Here, the RNA editome is systematically profiled on placentae from 9 patients with early-onset severe preeclampsia (EOSPE) and 32 normal controls, and a widespread RNA editing dysregulation in EOSPE has been identified. The mis-edited gene set is enriched with known preeclampsia-associated genes and differentially expressed genes in EOSPE. The “RNA editing events” at two microRNA binding sites in 3’-UTR of the LEP mRNA have been generated, which leads to increased expression level of LEP in trophoblast cells. Upregulation of LEP is also observed in the placentae of PE patients. These results suggest that widespread placental RNA editing may be involved in placental development and dysregulation of RNA editing in the placenta may contribute to the pathogenesis of preeclampsia.

2020-04-20 | GSE148241 | GEO

The landscape of A-to-I RNA editome from 462 individuals human genomes

Project description:A-to-I editing, as a post-transcriptional modification process mediated by ADAR, plays a crucial role in many biological process in metazoans. However, how and to what extent that A-to-I editing diversifies and shapes the population diversity at the RNA level is largely unknown. We employed 462 mRNA-sequencing data from five populations of the Geuvadis Project and identified 16,518 A-to-I editing sites, forming a landscape of RNA editome of the human genome. By exploration of RNA editing within and between populations, we discovered non-adaption of nonsynonymous editing in the evolution, and revealed geographic restriction of rare editing sites. Moreover, we showed that RNA editing can characterize the subtle but substantial divergence between different populations, especially those from different continents. Altogether, we demonstrated RNA editing can well depict the nature and structure of populations at RNA level, which provides insights into the process of how A-to-I editing shapes population diversity at transcriptomic level. Our work will facilitate the understanding of the landscape of RNA editome at population-scale, and be helpful to interpret difference in the distribution and prevalence of disease among individuals and across populations.

2017-08-31 | GSE103294 | GEO

The landscape of A-to-I RNA editome in mouse embryonic development

Project description:The landscape of A-to-I RNA editome in mouse embryonic development

| PRJNA507248 | ENA

Suppression of adenosine-to-inosine (A-to-I) RNA editome by death associated protein 3 (DAP3) promotes cancer progression

Project description:RNA editing introduces nucleotide changes in RNA sequences. Recent studies have reported that aberrant A-to-I RNA editing profiles are implicated in cancers. Albeit changes in expression and activity of ADAR genes are thought to have been responsible for the dysregulated RNA editome in diseases, they are not always correlated, indicating the involvement of secondary regulators. Here, we uncover DAP3 as a potent repressor of editing and a strong oncogene in cancer. DAP3 mainly interacts with the deaminase domain of ADAR2 and represses editing via disrupting association of ADAR2 with its target transcripts. PDZD7, an exemplary DAP3-repressed editing target, undergoes a protein recoding editing at stop codon [Stop →Trp (W)]. Because of editing suppression by DAP3, the unedited PDZD7WT, which is more tumorigenic than edited PDZD7Stop518W, is accumulated in tumors. In sum, cancer cells may acquire malignant properties for their survival advantage through suppressing RNA editome by DAP3.

2020-06-23 | GSE123020 | GEO

ADAR1-isoforms specific editome: RNA sequencing of A-to-I editing deficient mouse embryonic fibroblast transfected with ADAR1p150 or ADAR1p110 or RFP.

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

A to I editing of the 3'-UTR landscape regulates gene translation during retinal development

Project description:We used parallel ribosome profiling and RNA sequencing to investigate the relationship between RNA editing and translation. Through systematically profiling mouse tissues from different developmental stages, we found dynamic changes in A-to-I RNA editome during retinal development. Further analysis revealed that altered translational efficiency in retinal development correlates with dynamics of A-to-I RNA editome.

2023-10-01 | GSE104884 | GEO

Evaluation of the interplay between the ADAR editome and immunotherapy in melanoma

Project description:We evaluated the editome of melanoma cell lines generated from patients pre- and post-immunotherapy with immune checkpoint inhibitors by RNAseq. Our results reveal a differential editing in Alu sequences between samples pre-therapy and relapses during therapy with immune checkpoint inhibitors

2020-11-25 | GSE162095 | GEO

Placental Editome Profiling Reveals Widespread RNA-Editing Dysregulation in Preeclampsia

Project description:Placental Editome Profiling Reveals Widespread RNA-Editing Dysregulation in Preeclampsia

| PRJNA623568 | ENA

The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis

Project description:ADAR proteins alter gene expression both via catalyzing adenosine-to-inosine RNA editing and in an editing-independent manner by binding to target RNAs. Loss of ADARs affects neuronal function in all animals studied to date. To identify important neuronal targets in C. elegans, we performed the first unbiased assessment of the effects of ADR-2, the C. elegans editing enzyme, on the neural transcriptome. We identified the neural editome and gene expression changes associated with the loss of adr-2. As C. elegans lacking adr-2 exhibit reduced chemotaxis, our studies focused on targets that regulate this process. We identified an edited mRNA, clec-41, whose expression is dependent on ADR-2. Expressing clec-41 in adr-2 deficient neural cells restored chemotaxis. This study is the first of its kind in the RNA editing field to span from developing novel methodology for tissue-specific target identification to organismal behavior, significantly advancing our understanding of ADAR functions in neural cells.

2017-06-13 | GSE98869 | GEO

Trancriptome study in rhesus monkey

Project description:While the next generation sequencing technology is accelerating the discovery of sites in RNA editing, the strategies to accurately identify the editome, the mechanism by which its profile is maintained and its functional significance remain controversial. Here, 90bp × 2, paired-end, strand-specific, polyA-postive RNA-Seq were performed in 3 rhesus monkey tissues, and 90bp × 2, paired-end, whole exome sequencing was performed in blood cells. Combining genome-wide identification and other quality control in multiple tissues from the same individual, we identified a list of editing sites in coding regions from the rhesus macaque, one of our closest evolutionary relatives. Low-scale verification validated all of these sites and the corresponding levels of editing. The editome in macaque coding region suggests RNA editing as a type of controlled, conserved regulation shaped by purifying selection. This submission represents RNA-Seq: cerebellum, lung, kidney and heart component of study.

2014-03-03 | E-GEOD-42857 | biostudies-arrayexpress

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