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

作者：Jean‐Marc Celton, Sylvain Gaillard, Maryline Bruneau, Sandra Pelletier, Sébastien Aubourg, Marie‐Laure Martin‐Magniette, Lionel Navarro, François Laurens, Jean‐Pierre Renou · 发表于：New Phytologist · 年份：2014 · DOI：10.1111/nph.12787 · 被引用次数：64 · 研究领域：Plant Molecular Biology Research、Photosynthetic Processes and Mechanisms、Plant Reproductive Biology

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.