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RNA Isolation and Analysis of LncRNAs from Gametophytes of Maize

  • Linqian Han
  • Lin Li
  • Gary J. Muehlbauer
  • John E. Fowler
  • Matthew M. S. EvansEmail author
Part of the Methods in Molecular Biology book series (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.

Key words

LncRNAs Maize Gametophyte Pollen Embryo sac 

Notes

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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Linqian Han
    • 1
  • Lin Li
    • 1
  • Gary J. Muehlbauer
    • 2
    • 3
  • John E. Fowler
    • 4
  • Matthew M. S. Evans
    • 5
    Email author
  1. 1.College of Plant Sciences and TechnologyHuazhong Agricultural UniversityWuhanChina
  2. 2.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulUSA
  3. 3.Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulUSA
  4. 4.Department of Botany and Plant PathologyOregon State UniversityCorvallisUSA
  5. 5.Department of Plant BiologyCarnegie Institution for ScienceStanfordUSA

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