Authors: Alice Lunardon, Cristian Forestan, Silvia Farinati, Serena Varotto

Institutions: Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE) AgripolisUniversity of PadovaLegnaro (PD)Italy

Acknowledgements: Riccardo Aiese Cigliano and Walter Sanseverino

Publication: Plant Chromatin Dynamics

Date: October, 2017

Full paper: De Novo Identification of sRNA Loci and Non-coding RNAs by High-Throughput Sequencing


Non-coding RNA transcripts, such as long non-coding RNAs, miRNAs, siRNAs, and transposon-originating transcripts, are involved in the regulation of RNA stability, protein translation, and/or the modulation of chromatin states. RNA-Seq can be used to catalog this diversity of novel transcripts and a joint analysis of these transcriptomic data can provide useful insights into epigenetic regulation of dynamic responses such as the stress response, which may not be deciphered from individual analysis of single transcript categories. Here, we present a protocol that allows the identification and analysis of small RNAs and long non-coding RNAs, together with the comparison of these species between different sample types.