Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

Picardi, Ernesto; Horner, David S.; Chiara, Matteo; Schiavon, Riccardo; Valle, Giorgio; Pesole, Graziano

doi:10.1093/nar/gkq202

Cited by 131 publications

(112 citation statements)

References 48 publications

Supporting

Mentioning

108

Contrasting

Order By: Relevance

“…Among these transitions, although U-to-C and G-to-A changes were known, the preferences for these changes were first reported. These reports are not entirely consistent with previous findings in animals or plants, which show a preference for A-to-I (adenine to inosine) changes (Bahn et al 2012;Peng et al 2012) and C-to-U changes (Shikanai 2006;Picardi et al 2010), respectively. Four 15-bp motifs for purine transitions and pyrimidine transitions were identified, which were inconsistent with previous reports, indicating the diversity in the recognition of different substrates and the specificity in the recognition of conserved motif for RNA-editing enzyme complexes (Bahn et al 2012).…”

Section: Discussioncontrasting

confidence: 84%

Abundant and Selective RNA-Editing Events in the Medicinal Mushroom Ganoderma lucidum

et al. 2014

View full text Add to dashboard Cite

RNA editing is a widespread, post-transcriptional molecular phenomenon that diversifies hereditary information across various organisms. However, little is known about genome-scale RNA editing in fungi. In this study, we screened for fungal RNA editing sites at the genomic level in Ganoderma lucidum, a valuable medicinal fungus. On the basis of our pipeline that predicted the editing sites from genomic and transcriptomic data, a total of 8906 possible RNA-editing sites were identified within the G. lucidum genome, including the exon and intron sequences and the 59-/39-untranslated regions of 2991 genes and the intergenic regions. The major editing types included C-to-U, A-to-G, G-to-A, and U-to-C conversions. Four putative RNA-editing enzymes were identified, including three adenosine deaminases acting on transfer RNA and a deoxycytidylate deaminase. The genes containing RNA-editing sites were functionally classified by the Kyoto Encyclopedia of Genes and Genomes enrichment and gene ontology analysis. The key functional groupings enriched for RNA-editing sites included laccase genes involved in lignin degradation, key enzymes involved in triterpenoid biosynthesis, and transcription factors. A total of 97 putative editing sites were randomly selected and validated by using PCR and Sanger sequencing. We presented an accurate and large-scale identification of RNA-editing events in G. lucidum, providing global and quantitative cataloging of RNA editing in the fungal genome. This study will shed light on the role of transcriptional plasticity in the growth and development of G. lucidum, as well as its adaptation to the environment and the regulation of valuable secondary metabolite pathways. RNA editing is a post-transcriptional process that can enhance the diversity of gene products by altering RNA sequences. This can involve site-specific nucleotide modifications, nucleotide insertions/deletions, and nucleotide substitutions (Gott and Emeson 2000;Bass 2002;Farajollahi and Maas 2010). RNA editing can affect messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs, and small regulatory RNAs present in all cellular compartments and has been described in a wide range of organisms from viruses to fungi, mammals, and plants ( Gott and Emeson 2000;Gott 2003;Kawahara et al. 2007). The prevalent RNA-editing pathways in higher eukaryotes involves the deamination of cytidine (C) to create uridine (U) and deamination of adenosine (A) to create inosine (I) (Bass 2002;Gott 2003). The editing process generally involves a specificity factor (RNA or protein) that recognizes the editing site, as well as an enzyme, occasionally with other accessory factors, that catalyzes the reaction (Bass 2002). The functions of RNA editing include regulation of gene expression, increasing protein diversity and reversion of the effect of mutations in the genome (Gott and Emeson 2000;Gott 2003). In many cases, RNA editing is essential for correcting protein production (Young 1990) or for modulating the functional properties of proteins...

show abstract

Section: Discussioncontrasting

confidence: 84%

Abundant and Selective RNA-Editing Events in the Medicinal Mushroom Ganoderma lucidum

et al. 2014

View full text Add to dashboard Cite

show abstract

“…No other types of editing (e.g., U-to-C) were detected. The total number of editing sites in either Silene genome is lower than in any other angiosperm mitochondrial genome analyzed to date (Giege and Brennicke 1999;Notsu et al 2002;Handa 2003;Mower and Palmer 2006;Alverson et al 2010;Picardi et al 2010). This pattern results from both a reduced number of mitochondrial genes in Silene and a lower average density of editing sites within each gene (Table 1).…”

Section: Resultsmentioning

confidence: 74%

Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selectionvs. Retroprocessing as the Driving Force

et al. 2010

View full text Add to dashboard Cite

Theoretical arguments suggest that mutation rates influence the proliferation and maintenance of RNA editing. We identified RNA editing sites in five species within the angiosperm genus Silene that exhibit highly divergent mitochondrial mutation rates. We found that mutational acceleration has been associated with rapid loss of mitochondrial editing sites. In contrast, we did not find a significant difference in the frequency of editing in chloroplast genes, which lack the mutation rate variation observed in the mitochondrial genome. As found in other angiosperms, the rate of substitution at RNA editing sites in Silene greatly exceeds the rate at synonymous sites, a pattern that has previously been interpreted as evidence for selection against RNA editing. Alternatively, we suggest that editing sites may experience higher rates of C-to-T mutation than other portions of the genome. Such a pattern could be caused by gene conversion with reverse-transcribed mRNA (i.e., retroprocessing). If so, the genomic distribution of RNA editing site losses in Silene suggests that such conversions must be occurring at a local scale such that only one or two editing sites are affected at a time. Because preferential substitution at editing sites appears to occur in angiosperms regardless of the mutation rate, we conclude that mitochondrial rate accelerations within Silene have ''fast-forwarded'' a preexisting pattern but have not fundamentally changed the evolutionary forces acting on RNA editing sites.

show abstract

“…Knowledge of editing levels can have profound biological significance. Recently, de novo identification of editing sites was made possible by whole-transcriptome sequencing (RNA-seq) (Picardi et al 2010;Rosenberg et al 2010;Ju et al 2011;Li et al 2011). Quantitative estimation of editing levels may be achieved by sequencing a large number of reads via high-throughput sequencing.…”

mentioning

confidence: 99%

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

Bahn¹,

Lee²,

Li³

et al. 2011

Genome Res.

315

355

View full text Add to dashboard Cite

RNA editing enhances the diversity of gene products at the post-transcriptional level. Approaches for genome-wide identification of RNA editing face two main challenges: separating true editing sites from false discoveries and accurate estimation of editing levels. We developed an approach to analyze transcriptome sequencing data (RNA-seq) for global identification of RNA editing in cells for which whole-genome sequencing data are available. We applied the method to analyze RNA-seq data of a human glioblastoma cell line, U87MG. Around 10,000 DNA-RNA differences were identified, the majority being putative A-to-I editing sites. These predicted A-to-I events were associated with a low false-discovery rate (~5%). Moreover, the estimated editing levels from RNA-seq correlated well with those based on traditional clonal sequencing. Our results further facilitated unbiased characterization of the sequence and evolutionary features flanking predicted A-to-I editing sites and discovery of a conserved RNA structural motif that may be functionally relevant to editing. Genes with predicted A-to-I editing were significantly enriched with those known to be involved in cancer, supporting the potential importance of cancer-specific RNA editing. A similar profile of DNA-RNA differences as in U87MG was predicted for another RNA-seq data set obtained from primary breast cancer samples. Remarkably, significant overlap exists between the putative editing sites of the two transcriptomes despite their difference in cell type, cancer type, and genomic backgrounds. Our approach enabled de novo identification of the RNA editome, which sets the stage for further mechanistic studies of this important step of post-transcriptional regulation.

show abstract

Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

Cited by 131 publications

References 48 publications

Abundant and Selective RNA-Editing Events in the Medicinal Mushroom Ganoderma lucidum

Abundant and Selective RNA-Editing Events in the Medicinal Mushroom Ganoderma lucidum

Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selectionvs. Retroprocessing as the Driving Force

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

Contact Info

Product

Resources

About