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

Publication: Plant Chromatin Dynamics

Date: October 2017

Full paper: https://link.springer.com/protocol/10.1007/978-1-4939-7318-7_17

Abstract:

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.