ArticleGenome biology2014
Alu elements shape the primate transcriptome by cis-regulation of RNA editing.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
65 citing papers in PubMed, 114 citations in OpenAlex.
- TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data.Genome biology · 2026Article
- Repeats mimic pathogen-associated patterns across a vast evolutionary landscape.Cell genomics · 2025Article
- Correlation of extracellular vesicle Alu RNA with brain aging and neuronal injury: a potential biomarker for brain aging.Annals of medicine · 2025Article
- Nanoparticle Delivery of Alu RNA Adjuvants Enhances Vaccine Immunogenicity.ACS applied materials & interfaces · 2025Article
- Alu RNA pseudoknot alterations influence SRP9/SRP14 association.RNA (New York, N.Y.) · 2025Article
- ADARs: pleiotropy in function, versatility in application.Nucleic acids research · 2025Review
- Genome sequencing of3 Biotech · 2024Article
- Alu insertion-mediated dsRNA structure formation with pre-existing Alu elements as a disease-causing mechanism.American journal of human genetics · 2024Article
- RNA Editing in Cancer Progression.Cancers · 2023Review
- Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression.RNA (New York, N.Y.) · 2023Article
- RNA Editing Enzyme ADAR1 Suppresses the Mobility of Cancer Cells via ARPIN.Molecules and cells · 2023Article
- Expanding the proteome: A-to-I RNA editing provides an adaptive advantage.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.Communications biology · 2022Article
- Reduction of A-to-I RNA editing in the failing human heart regulates formation of circular RNAs.Basic research in cardiology · 2022Article
- The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology.International journal of molecular sciences · 2022Review
- Landscape of adenosine-to-inosine RNA recoding across human tissues.Nature communications · 2022Article
- Genome-wide perturbations of Alu expression and Alu-associated post-transcriptional regulations distinguish oligodendroglioma from other gliomas.Communications biology · 2022Article
- Phosphodiesterase 8A to discriminate in blood samples depressed patients and suicide attempters from healthy controls based on A-to-I RNA editing modifications.Translational psychiatry · 2021Article
- Retrotransposons as Drivers of Mammalian Brain Evolution.Life (Basel, Switzerland) · 2021Review
- Programmable System of Cas13-Mediated RNA Modification and Its Biological and Biomedical Applications.Frontiers in cell and developmental biology · 2021Review
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA editing by adenosine to inosine deamination is a widespread phenomenon, particularly frequent in the human transcriptome, largely due to the presence of inverted Alu repeats and their ability to form double-stranded structures--a requisite for ADAR editing. While several hundred thousand editing sites have been identified within these primate-specific repeats, the function of Alu-editing has yet to be elucidated.
resultsWe show that inverted Alu repeats, expressed in the primate brain, can induce site-selective editing in cis on sites located several hundred nucleotides from the Alu elements. Furthermore, a computational analysis, based on available RNA-seq data, finds that site-selective editing occurs significantly closer to edited Alu elements than expected. These targets are poorly edited upon deletion of the editing inducers, as well as in homologous transcripts from organisms lacking Alus. Sequences surrounding sites near edited Alus in UTRs, have been subjected to a lesser extent of evolutionary selection than those far from edited Alus, indicating that their editing generally depends on cis-acting Alus. Interestingly, we find an enrichment of primate-specific editing within encoded sequence or the UTRs of zinc finger-containing transcription factors.
conclusionsWe propose a model whereby primate-specific editing is induced by adjacent Alu elements that function as recruitment elements for the ADAR editing enzymes. The enrichment of site-selective editing with potentially functional consequences on the expression of transcription factors indicates that editing contributes more profoundly to the transcriptomic regulation and repertoire in primates than previously thought.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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 OpenQuestion graph.