title: Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.
abstract: RNA editing is a widespread post-transcriptional molecular phenomenon that can increase proteomic diversity, by modifying the sequence of completely or partially non-functional primary transcripts, through a variety of mechanistically and evolutionarily unrelated pathways. Editing by base substitution has been investigated in both animals and plants. However, conventional strategies based on directed Sanger sequencing are time-consuming and effectively preclude genome wide identification of RNA editing and assessment of partial and tissue-specific editing sites. In contrast, the high-throughput RNA-Seq approach allows the generation of a comprehensive landscape of RNA editing at the genome level. Short reads from Solexa/Illumina GA and ABI SOLiD platforms have been used to investigate the editing pattern in mitochondria of Vitis vinifera providing significant support for 401 C-to-U conversions in coding regions and an additional 44 modifications in non-coding RNAs. Moreover, 76% of all C-to-U conversions in coding genes represent partial RNA editing events and 28% of them were shown to be significantly tissue specific. Solexa/Illumina and SOLiD platforms showed different characteristics with respect to the specific issue of large-scale editing analysis, and the combined approach presented here reduces the false positive rate of discovery of editing events.
authors.affiliation: Dipartimento di Biochimica e Biologia Molecolare E. Quagliariello, Università degli Studi di Bari, Bari, Italy.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Picardi
authors.forename: David S
authors.initials: DS
authors.lastname: Horner
authors.forename: Matteo
authors.initials: M
authors.lastname: Chiara
authors.forename: Riccardo
authors.initials: R
authors.lastname: Schiavon
authors.forename: Giorgio
authors.initials: G
authors.lastname: Valle
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D020137:Base Pair Mismatch; D004272:DNA, Mitochondrial / Q000737:chemistry*; D018744:DNA, Plant / Q000737:chemistry; D050259:Genes, Mitochondrial; D054629:Genome, Mitochondrial; D023281:Genomics; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D017393:RNA Editing; D000077278:RNA, Mitochondrial; D018749:RNA, Plant / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D027843:Vitis / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial; D018744:DNA, Plant; D000077278:RNA, Mitochondrial; D018749:RNA, Plant; D012313:RNA
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