ArticleRNA biology2015
Genome-wide identification and characterization of tissue-specific RNA editing events in D. melanogaster and their potential role in regulating alternative splicing.
Article in RNA biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 44 citations in OpenAlex.
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- Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes.International journal of molecular sciences · 2023Review
- Epitranscriptomics as a New Layer of Regulation of Gene Expression in Skeletal Muscle: Known Functions and Future Perspectives.International journal of molecular sciences · 2023Review
- e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.Nucleic acids research · 2023Article
- Article
- Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis.RNA (New York, N.Y.) · 2023Article
- ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence.Nucleic acids research · 2022Article
- Women in the European Virus Bioinformatics Center.Viruses · 2022Article
- Roles of peripheral clocks: lessons from the fly.FEBS letters · 2022Review
- The mJournal of biomedical science · 2021Review
- CoBold: a method for identifying different functional classes of transient RNA structure features that can impact RNA structure formation in vivo.Nucleic acids research · 2021Article
- A-to-I RNA editing in honeybees shows signals of adaptation and convergent evolution.iScience · 2021Article
- ADAR-deficiency perturbs the global splicing landscape in mouse tissues.Genome research · 2020Article
- Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control.International journal of molecular sciences · 2020Review
- Zinc Finger RNA-Binding Protein Zn72D Regulates ADAR-Mediated RNA Editing in Neurons.Cell reports · 2020Article
- Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development.Nature communications · 2020Article
- RNA editing in the forefront of epitranscriptomics and human health.Journal of translational medicine · 2019Review
- A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing.Genome research · 2019Article
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA editing is a widespread mechanism that plays a crucial role in diversifying gene products. Its abundance and importance in regulating cellular processes were revealed using new sequencing technologies. The majority of these editing events, however, cannot be associated with regulatory mechanisms. We use tissue-specific high-throughput libraries of D. melanogaster to study RNA editing. We introduce an analysis pipeline that utilises large input data and explicitly captures ADAR's requirement for double-stranded regions. It combines probabilistic and deterministic filters and can identify RNA editing events with a low estimated false positive rate. Analyzing ten different tissue types, we predict 2879 editing sites and provide their detailed characterization. Our analysis pipeline accurately distinguishes genuine editing sites from SNPs and sequencing and mapping artifacts. Our editing sites are 3 times more likely to occur in exons with multiple splicing acceptor/donor sites than in exons with unique splice sites (p-value < 2.10(-15)). Furthermore, we identify 244 edited regions where RNA editing and alternative splicing are likely to influence each other. For 96 out of these 244 regions, we find evolutionary evidence for conserved RNA secondary-structures near splice sites suggesting a potential regulatory mechanism where RNA editing may alter splicing patterns via changes in local RNA structure.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.