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Bioinformatics Approaches to Studying Plant Long Noncoding RNAs (lncRNAs): Identification and Functional Interpretation of lncRNAs from RNA-Seq Data Sets

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Plant Long Non-Coding RNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1933))

Abstract

Long noncoding RNAs (lncRNAs) play important roles in regulating various biological processes including growth and stress responses in plants. RNA-seq data sets provide a good resource to exploring the noncoding transcriptome and studying their comprehensive interactions with the coding transcriptome. Here, we describe computational procedures for studying plant lncRNAs including long intergenic noncoding RNAs (lincRNAs) and long noncoding natural antisense transcripts (lncNATs). Bioinformatics tools for transcriptome assembly, lncRNA identification, and functional interpretations are included. Finally, we also introduce PLncDB, a user-friendly database that provides comprehensive information of plant lncRNAs for researchers to compare their own data sets to those in public database.

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Acknowledgment

We thank Jun Liu and Huan Wang for developing the above bioinformatics methods for lincRNA and lncNAT analyses and Jingjing Jin for constructing PLncDB. This work was funded in part by Singapore NRF RSSS Grant NRF-RSSS-002.

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Authors and Affiliations

  1. Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, USA

    Hai-Xi Sun & Nam-Hai Chua

  2. TEMASEK Life Sciences Laboratory, National University of Singapore, Singapore, Singapore

    Nam-Hai Chua

Authors
  1. Hai-Xi Sun
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  2. Nam-Hai Chua
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Correspondence to Nam-Hai Chua .

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Editors and Affiliations

  1. Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China

    Julia A. Chekanova  & Hsiao-Lin V. Wang  & 

  2. Department of Biology, Emory University, Atlanta, Georgia, USA

    Hsiao-Lin V. Wang

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Sun, HX., Chua, NH. (2019). Bioinformatics Approaches to Studying Plant Long Noncoding RNAs (lncRNAs): Identification and Functional Interpretation of lncRNAs from RNA-Seq Data Sets. In: Chekanova, J.A., Wang, HL.V. (eds) Plant Long Non-Coding RNAs. Methods in Molecular Biology, vol 1933. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9045-0_11

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  • DOI: https://doi.org/10.1007/978-1-4939-9045-0_11

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9044-3

  • Online ISBN: 978-1-4939-9045-0

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