Widespread anti‐sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post‐transcriptional control

• Published in: The New phytologist Vol. 203; no. 1; pp. 287 - 299
• Main Authors: Celton, Jean‐Marc, Gaillard, Sylvain, Bruneau, Maryline, Pelletier, Sandra, Aubourg, Sébastien, Martin‐Magniette, Marie‐Laure, Navarro, Lionel, Laurens, François, Renou, Jean‐Pierre
• Format: Journal Article
• Language: English
• Published: England William Wesley and Son 01.07.2014; New Phytologist Trust; Wiley Subscription Services, Inc; Wiley
• Subjects: 3' Untranslated regions; annuals; anti‐sense; apples; Arabidopsis thaliana; Biogenesis; Body organs; Correlation; Coverage; DNA microarrays; Fruits; Gene expression; Gene Expression Regulation, Plant; Gene regulation; Genes; Genetic loci; Genomes; High-Throughput Nucleotide Sequencing; Life Sciences; Malus; Malus - genetics; Malus domestica; microarray technology; nat‐siRNA; Oligonucleotide Array Sequence Analysis; Organs; Oryza sativa; Percentages; phenotype; Phenotypes; rice; RNA; RNA interference; RNA Processing, Post-Transcriptional; RNA, Antisense - genetics; RNA, Plant - genetics; RNA, Small Interfering - genetics; RNA-mediated interference; Seeds; sense; Sequence Analysis, RNA; Sequencing; siRNA; Small interfering RNA; small‐RNA; Transcription; transcription (genetics); Transcription, Genetic; transcriptome; Transcriptomes; small-RNA; sense; anti-sense; atlas; transcriptome; nat-siRNA
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/nph.12787

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.