RNA Isolation and Analysis of LncRNAs from Gametophytes of Maize

Linqian Han; Lin Li; Gary J. Muehlbauer; John E. Fowler; Matthew M.S. Evans

doi:10.1007/978-1-4939-9045-0_4

RNA Isolation and Analysis of LncRNAs from Gametophytes of Maize

Linqian Han, Lin Li, Gary J. Muehlbauer, John E. Fowler, Matthew M.S. Evans

Agronomy and Plant Genetics

Research output: Chapter in Book/Report/Conference proceeding › Chapter

2 Scopus citations

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.

Original language	English (US)
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	67-86
Number of pages	20
DOIs	https://doi.org/10.1007/978-1-4939-9045-0_4
State	Published - 2019

Publication series

Name	Methods in Molecular Biology
Volume	1933
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Bibliographical note

Funding Information:
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).

Publisher Copyright:
© 2019, Springer Science+Business Media, LLC, part of Springer Nature.

Keywords

Embryo sac
Gametophyte
LncRNAs
Maize
Pollen

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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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KW - Pollen

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RNA Isolation and Analysis of LncRNAs from Gametophytes of Maize

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