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

  • Alice Lunardon
  • Cristian Forestan
  • Silvia Farinati
  • Serena Varotto
Part of the Methods in Molecular Biology book series (MIMB, volume 1675)

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.

Key words

Epigenetic regulation lncRNA Non-coding RNA RNA-Seq sRNA Transcriptome analysis Transposable elements 

Notes

Acknowledgments

The authors would like to thank Riccardo Aiese Cigliano and Walter Sanseverino (Sequentia Biotech) for their precious collaboration during the whole project. This work was supported by EC grant AENEAS and Italian MIUR-CNR EPIGEN Flagship Project to SV.

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Alice Lunardon
    • 1
  • Cristian Forestan
    • 1
  • Silvia Farinati
    • 1
  • Serena Varotto
    • 1
  1. 1.Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE) AgripolisUniversity of PadovaLegnaro (PD)Italy

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