Phytohormone-responsive long noncoding RNAs in Brachypodium distachyon

High-throughput sequencing technologies brought a deeper insight into cell transcriptomes, revealing a much more complex scenario in RNA molecules biogenesis and functions. While coding RNA counts for only 2% of the transcribed genome, noncoding RNAs, and in particular long noncoding RNAs (lncRNAs), despite their active transcription still represent an emerging field of research. This is particularly true in plants, where lncRNAs have been investigated at genomic level in a very limited number of species . Recently, sex-biased expression of lincRNAs in mice, rat and human liver was shown, where lincRNAs are regulated in a growth-hormone dependent manner. Similarly, several small noncoding RNAs were shown to be induced specifically under plant hormones treatments. In this study we have identified a large set of phytohormone-responsive lncRNAs in Brachypodium distachyon (Bd), a model species for temperate cereals, updating the current lncRNAs catalogue for this species (Bertolini et al. submitted). A lncRNAs genome-wide annotation has been conducted using publicly available RNA-seq data from 12 experiments, representing treatments with the various phytohormones, such as auxin, cytokinin, gibberellin, brassinosteroid, salicylic acid, abscisic acid, jasmonate and ethylene. In total 1,731 novel bona-fide lncRNAs have been identified and described, showing their genomic organization and their expression profiles. To better investigate the regulatory roles of lncRNA-mediated gene regulation, potential lncRNA targets as well as the promoter sequences of phytohormone-responsive lncRNAs have been examined. With this study we contribute to highlight the regulatory networks and cross-talk between different RNA molecules associated with plant hormones, unveiling the complex mechanisms at the base of hormone signalling and plant development.