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Plant Long Non-Coding RNAs pp 67–86Cite as

RNA Isolation and Analysis of LncRNAs from Gametophytes of Maize

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

Abstract

The explosion of RNA-Seq data has enabled the identification of expressed genes without relying on gene models with biases toward open reading frames, allowing the identification of many more long noncoding RNAs (lncRNAs) in eukaryotes. Various tissue enrichment strategies and deep sequencing have also enabled the identification of an extensive list of genes expressed in maize gametophytes, tissues that are intractable to both traditional genetic and gene expression analyses. However, the function of very few genes from the lncRNA and gametophyte sets (or from their intersection) has been tested. Methods for isolating and identifying lncRNAs from gametophyte samples of maize are described here. This method is transferable to any maize gametophyte mutant enabling the development of gene networks involving both protein-coding genes and lncRNAs. Additionally, these methods can be adapted to apply to other grass model systems to test for evolutionary conservation of lncRNA expression patterns.

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Acknowledgments

We thank Z. Vejlupkova and R. Cole for their contributions to the development of the RNA isolation and library preparation methodology. This work was supported by National Science Foundation Plant Genome Research Program Awards, DBI-0701731 and DBI-1340050, to Matthew Evans and by Huazhong Agricultural University Scientific & Technological Self-innovation Foundation to Lin Li and Linqian Han (Program No. 2662016PY096).

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Author notes

  1. Linqian Han & Lin Li

    Present address: College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, China

Authors and Affiliations

  1. Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA

    Gary J. Muehlbauer

  2. Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA

    Gary J. Muehlbauer

  3. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA

    John E. Fowler

  4. Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA

    Matthew M. S. Evans

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  1. Linqian Han
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  2. Lin Li
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  3. Gary J. Muehlbauer
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  4. John E. Fowler
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  5. Matthew M. S. Evans
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Corresponding author

Correspondence to Matthew M. S. Evans .

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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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Han, L., Li, L., Muehlbauer, G.J., Fowler, J.E., Evans, M.M.S. (2019). RNA Isolation and Analysis of LncRNAs from Gametophytes of Maize. 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_4

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  • DOI: https://doi.org/10.1007/978-1-4939-9045-0_4

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9044-3

  • Online ISBN: 978-1-4939-9045-0

  • eBook Packages: Springer Protocols

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