ArticleBMC genetics2020
Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana.
Article in BMC genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 20 citations in OpenAlex.
- On the origin, evolution, and maintenance of RNA editing.Nucleic acids research · 2025Review
- Analysis of the mitochondrial genome of theFrontiers in plant science · 2025Article
- Convergent evolution of allele-specific gene expression that leads to non-small cell lung cancer in different human populations.Journal of applied genetics · 2024Article
- A-to-I RNA editing shows dramatic up-regulation in osteosarcoma and broadly regulates tumor-related genes by altering microRNA target regions.Journal of applied genetics · 2023Article
- C-to-U RNA deamination is the driving force accelerating SARS-CoV-2 evolution.Life science alliance · 2023Article
- Exploring the RNA Editing Events and Their Potential Regulatory Roles in Tea Plant (International journal of molecular sciences · 2022Article
- RNA editing detection in SARS-CoV-2 transcriptome should be different from traditional SNV identification.Journal of applied genetics · 2022Article
- Gene expression variation explains maize seed germination heterosis.BMC plant biology · 2022Article
- An evolutionarily conserved mechanism that amplifies the effect of deleterious mutations in osteosarcoma.Molecular genetics and genomics : MGG · 2022Article
- COVID-19 and its genomic variants: Molecular pathogenesis and therapeutic interventions.EXCLI journal · 2022Review
- Mutation profiling of a limbless pig reveals genome-wide regulation of RNA processing related to bone development.Journal of applied genetics · 2021Article
- Context-dependent and -independent selection on synonymous mutations revealed by 1,135 genomes of Arabidopsis thaliana.BMC ecology and evolution · 2021Article
- Maize kernel development.Molecular breeding : new strategies in plant improvement · 2021Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundC-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. The biological functions of a fraction of C-to-U editing sites are continuously discovered by case studies. However, at genome-wide level, the cis and trans determinants affecting the occurrence or editing levels of these C-to-U events are relatively less studied. What is known is that the PPR (pentatricopeptide repeat) proteins are the main trans-regulatory elements responsible for the C-to-U conversion, but other determinants especially the cis-regulatory elements remain largely uninvestigated.
resultsBy analyzing the transcriptome and translatome data in Arabidopsis thaliana roots and shoots, combined with RNA-seq data from hybrids of Arabidopsis thaliana and Arabidopsis lyrata, we perform genome-wide investigation on the cis elements and trans-regulatory elements that potentially affect C-to-U editing events. An upstream guanosine or double-stranded RNA (dsRNA) regions are unfavorable for editing events. Meanwhile, many genes including the transcription factors may indirectly play regulatory roles in trans.
conclusionsThe 5-prime thymidine facilitates editing and dsRNA structures prevent editing in cis. Many transcription factors affect editing in trans. Although the detailed molecular mechanisms underlying the cis and trans regulation remain to be experimentally verified, our findings provide novel aspects in studying the botanical C-to-U RNA editing events.
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