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

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Plant Chromatin Dynamics

Part of the book series: Methods in Molecular Biology ((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.

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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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Author notes

  1. Alice Lunardon and Cristian Forestan contributed equally to this work.

Authors and Affiliations

  1. Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE) Agripolis, University of Padova, Viale dell’Università 16, 35020, Legnaro (PD), Italy

    Alice Lunardon, Cristian Forestan, Silvia Farinati & Serena Varotto

Authors
  1. Alice Lunardon
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  2. Cristian Forestan
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  3. Silvia Farinati
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  4. Serena Varotto
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Corresponding author

Correspondence to Serena Varotto .

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Editors and Affiliations

  1. Department of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands

    Marian Bemer

  2. Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland

    Célia Baroux

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Lunardon, A., Forestan, C., Farinati, S., Varotto, S. (2018). De Novo Identification of sRNA Loci and Non-coding RNAs by High-Throughput Sequencing. In: Bemer, M., Baroux, C. (eds) Plant Chromatin Dynamics. Methods in Molecular Biology, vol 1675. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7318-7_17

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  • DOI: https://doi.org/10.1007/978-1-4939-7318-7_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7317-0

  • Online ISBN: 978-1-4939-7318-7

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