title: Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control.
abstract: Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined. Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (sRNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple (Malus × domestica). The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3'UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21-23 nt) and long (> 30 nt) siRNAs, and that the sRNA coverage depth varies with the level of AS transcript expression. Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of sRNA biogenesis in plants.
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 49071, Beaucouzé, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Celton
authors.forename: Sylvain
authors.initials: S
authors.lastname: Gaillard
authors.forename: Maryline
authors.initials: M
authors.lastname: Bruneau
authors.forename: Sandra
authors.initials: S
authors.lastname: Pelletier
authors.forename: Sébastien
authors.initials: S
authors.lastname: Aubourg
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Martin-Magniette
authors.forename: Lionel
authors.initials: L
authors.lastname: Navarro
authors.forename: François
authors.initials: F
authors.lastname: Laurens
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Renou
mesh_terms: D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D027845:Malus / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012323:RNA Processing, Post-Transcriptional; D016372:RNA, Antisense / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D016372:RNA, Antisense; D018749:RNA, Plant; D034741:RNA, Small Interfering
keywords: anti-sense; atlas; nat-siRNA; sense; small-RNA; transcriptome