These authors contributed equally to this work.
Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control
Article first published online: 1 APR 2014
© 2014 INRA. New Phytologist © 2014 New Phytologist Trust
Volume 203, Issue 1, pages 287–299, July 2014
How to Cite
Celton, J.-M., Gaillard, S., Bruneau, M., Pelletier, S., Aubourg, S., Martin-Magniette, M.-L., Navarro, L., Laurens, F. and Renou, J.-P. (2014), Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control. New Phytologist, 203: 287–299. doi: 10.1111/nph.12787
- Issue published online: 28 MAY 2014
- Article first published online: 1 APR 2014
- Manuscript Accepted: 26 FEB 2014
- Manuscript Received: 29 JAN 2014
- Institut National de la Recherche Agronomique, Plant Biology and Breeding division
- Pays de Loire Region
- 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.