ArticlePloS one2018
Genome-wide identification and analysis of A-to-I RNA editing events in bovine by transcriptome sequencing.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 43 citations in OpenAlex.
- A dynamic RNA editing landscape in porcine spleen highlights a post-transcriptional mechanism for immune maturation.Molecular genetics and genomics : MGG · 2026Article
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- Selection signature analysis in chickens divergently selected for growth rate reveals novel candidate genes regulating fat deposition.BMC genomics · 2025Article
- Identification of RNA Editing Sites Reveals Functional Modifications with the Addition of Methionine to the Daily Rations of Yaks.Animals : an open access journal from MDPI · 2025Article
- Genomic Landscape and Regulation of RNA Editing in Pekin Ducks Susceptible to Duck Hepatitis A Virus Genotype 3 Infection.International journal of molecular sciences · 2024Article
- RNA-DNA differences in variant calls from cattle tissues result in erroneous eQTLs.BMC genomics · 2024Article
- Detection of Developmental Asexual Stage-Specific RNA Editing Events inMicroorganisms · 2024Article
- Global A-to-I RNA editing during myogenic differentiation of goat MuSCs.Frontiers in veterinary science · 2024Article
- RNA-Seq based selection signature analysis for identifying genomic footprints associated with the fat-tail phenotype in sheep.Frontiers in veterinary science · 2024Article
- Fat-tail allele-specific expression genes may affect fat deposition in tail of sheep.PloS one · 2024Article
- A novel computational method enables RNA editome profiling during human hematopoiesis from scRNA-seq data.Scientific reports · 2023Article
- Expression and Functional Analysis ofAnimals : an open access journal from MDPI · 2023Article
- Characterization of A-to-I Editing in Pigs under a Long-Term High-Energy Diet.International journal of molecular sciences · 2023Article
- The Profiles and Functions of RNA Editing Sites Associated with High-Altitude Adaptation in Goats.International journal of molecular sciences · 2023Article
- Intra- and Interspecies RNA-Seq Based Variants in the Lactation Process of Ruminants.Animals : an open access journal from MDPI · 2022Article
- Genome-wide detection of RNA editing events during the hair follicles cycle of Tianzhu white yak.BMC genomics · 2022Article
- Change of Heart: the Epitranscriptome of Small Non-coding RNAs in Heart Failure.Current heart failure reports · 2022Review
- Characterization of RNA Editome in the Mammary Gland of Yaks during the Lactation and Dry Periods.Animals : an open access journal from MDPI · 2022Article
- Screening and Verification of Molecular Markers and Genes Related to Salt-Alkali Tolerance inFrontiers in genetics · 2022Article
- Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA editing increases the diversity of the transcriptome and proteome. Adenosine-to-inosine (A-to-I) editing is the predominant type of RNA editing in mammals and it is catalyzed by the adenosine deaminases acting on RNA (ADARs) family. Here, we used a largescale computational analysis of transcriptomic data from brain, heart, colon, lung, spleen, kidney, testes, skeletal muscle and liver, from three adult animals in order to identify RNA editing sites in bovine. We developed a computational pipeline and used a rigorous strategy to identify novel editing sites from RNA-Seq data in the absence of corresponding DNA sequence information. Our methods take into account sequencing errors, mapping bias, as well as biological replication to reduce the probability of obtaining a false-positive result. We conducted a detailed characterization of sequence and structural features related to novel candidate sites and found 1,600 novel canonical A-to-I editing sites in the nine bovine tissues analyzed. Results show that these sites 1) occur frequently in clusters and short interspersed nuclear elements (SINE) repeats, 2) have a preference for guanines depletion/enrichment in the flanking 5'/3' nucleotide, 3) occur less often in coding sequences than other regions of the genome, and 4) have low evolutionary conservation. Further, we found that a positive correlation exists between expression of ADAR family members and tissue-specific RNA editing. Most of the genes with predicted A-to-I editing in each tissue were significantly enriched in biological terms relevant to the function of the corresponding tissue. Lastly, the results highlight the importance of the RNA editome in nervous system regulation. The present study extends the list of RNA editing sites in bovine and provides pipelines that may be used to investigate the editome in other organisms.
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