ArticleProceedings of the National Academy of Sciences of the United States of America2013
Characterization and comparison of human nuclear and cytosolic editomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Knockdown of RNA editing proteins reshapes the HepaRG transcriptome and pharmacogene expression.Scientific reports · 2026Article
- Murine norovirus mutants adapted to replicate in human cells reveal a post-entry restriction.Journal of virology · 2024Article
- Murine norovirus mutants adapted to replicate in human cells reveal a post-entry restriction.bioRxiv : the preprint server for biology · 2024Article
- Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections.BMC genomics · 2023Article
- Predicting functional consequences of SNPs on mRNA translation via machine learning.Nucleic acids research · 2023Article
- Comparative functional RNA editomes of neural differentiation from human PSCs.Life medicine · 2022Article
- A hierarchy in clusters of cephalopod mRNA editing sites.Scientific reports · 2022Article
- ADAR Editing in Viruses: An Evolutionary Force to Reckon with.Genome biology and evolution · 2021Review
- Cortical cellular diversity and development in schizophrenia.Molecular psychiatry · 2021Review
- Human A-to-I RNA editing SNP loci are enriched in GWAS signals for autoimmune diseases and under balancing selection.Genome biology · 2020Article
- Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris).Scientific reports · 2020Article
- A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals.Genome biology and evolution · 2020Article
- Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation.Genome research · 2020Article
- Article
- Evolution of a reverse transcriptase to map NNature methods · 2019Article
- A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations.Genome research · 2019Article
- CREDO: Highly confident disease-relevant A-to-I RNA-editing discovery in breast cancer.Scientific reports · 2019Article
- WidespreadRNA (New York, N.Y.) · 2019Article
- RNA Biology Provides New Therapeutic Targets for Human Disease.Frontiers in genetics · 2019Review
- A-to-I RNA editing - immune protector and transcriptome diversifier.Nature reviews. Genetics · 2018Review
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1 author.
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Abstract
We developed a robust computational statistical framework to identify RNA editing events from RNA-Seq data with high specificity. Our approach handles several outstanding challenges of genome-wide editing analyses, including the effect of editing on read alignment and the utilization of redundant reads. By applying this framework, we characterized the nuclear and cytosolic editomes of seven human cell lines. We found that 93.8-99.2% of the editing events are A-to-G (or A-to-I). Nuclear transcriptomes contain many more editing events than cytosolic transcriptomes. Most of the sites exhibiting nucleus-specific editing are in introns or novel intergenic transcripts that are preferentially localized in the nucleus regardless of their editing status, arguing against the role of editing in nuclear retention. In contrast, many sites that exhibit cytosol-specific editing show comparable nuclear and cytosolic expression, suggesting the differential subcellular compartmentalization of the edited and the unedited alleles. We found that RNA editing is globally associated with the modification of microRNA regulation in 3' untranslated regions, whereas editing events in coding regions are rare and tend to be synonymous. Interestingly, A-to-G editing at derived alleles in the human lineage tends to result in reversion back to the ancestral forms at the RNA level. This suggests that editing can mediate RNA memory on evolutionary time-scales to maintain ancestral genetic information.
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