Skip to main content
Book cover

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

RNA Isolation and Analysis of LncRNAs from Gametophytes of Maize

  • Protocol

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

This is a preview of subscription content, access via your institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-1-4939-9045-0_4
  • Chapter length: 20 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   169.00
Price excludes VAT (USA)
  • ISBN: 978-1-4939-9045-0
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Hardcover Book
USD   219.99
Price excludes VAT (USA)
Learn about institutional subscriptions
Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Batista PJ, Chang HY (2013) Long noncoding RNAs: cellular address codes in development and disease. Cell 152(6):1298–1307. https://doi.org/10.1016/j.cell.2013.02.012

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  2. Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Ann Rev Biochem 81:145–166. https://doi.org/10.1146/annurev-biochem-051410-092902

    CrossRef  CAS  PubMed  Google Scholar 

  3. Su Y, Zhang C, Wei Q (2014) Advances of long noncoding RNA. Acta Botanica Boreali-Occidentalia Sinica 11:31

    CAS  Google Scholar 

  4. Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, Barrette TR, Prensner JR, Evans JR, Zhao S, Poliakov A, Cao X, Dhanasekaran SM, Wu YM, Robinson DR, Beer DG, Feng FY, Iyer HK, Chinnaiyan AM (2015) The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 47(3):199–208. https://doi.org/10.1038/ng.3192

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  5. Wen K, Yang L, Xiong T, Di C, Ma D, Wu M, Xue Z, Zhang X, Long L, Zhang W, Zhang J, Bi X, Dai J, Zhang Q, Lu ZJ, Gao G (2016) Critical roles of long noncoding RNAs in Drosophila spermatogenesis. Genome Res 26(9):1233–1244. https://doi.org/10.1101/gr.199547.115

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  6. Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331(6013):76–79. https://doi.org/10.1126/science.1197349

    CrossRef  CAS  PubMed  Google Scholar 

  7. Chekanova JA (2015) Long non-coding RNAs and their functions in plants. Curr Opin Plant Biol 27:207–216. https://doi.org/10.1016/j.pbi.2015.08.003

    CrossRef  CAS  PubMed  Google Scholar 

  8. Chettoor AM, Givan SA, Cole RA, Coker CT, Unger-Wallace E, Vejlupkova Z, Vollbrecht E, Fowler JE, Evans M (2014) Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes. Genome Biol 15(7):414. https://doi.org/10.1186/s13059-014-0414-2

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kranz E, Bautor J, Lorz H (1991) In vitro ferilization of single, isolated gametes of maize mediated by electrofusion. Sex Plant Reprod 4:12–16

    Google Scholar 

  10. Yang H, Kaur N, Kiriakopolos S, McCormick S (2006) EST generation and analyses towards identifying female gametophyte-specific genes in Zea mays L. Planta 224(5):1004–1014

    CrossRef  CAS  PubMed  Google Scholar 

  11. Schreiber DN, Dresselhaus T (2003) In vitro pollen germination and transient transformation of Zea mays and other plant species. Plant Mol Biol Rep 21:31–41

    CrossRef  Google Scholar 

  12. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  13. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  14. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111. https://doi.org/10.1093/bioinformatics/btp120

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079. https://doi.org/10.1093/bioinformatics/btp352

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  16. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621–628. https://doi.org/10.1038/nmeth.1226

    CrossRef  CAS  PubMed  Google Scholar 

  17. Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MMS, Scanlon MJ, Yu J, Schnable PS, Timmermans MC, Springer NM, Muehlbauer GJ (2014) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol 15(2):R40. https://doi.org/10.1186/gb-2014-15-2-r40

    CrossRef  PubMed  PubMed Central  Google Scholar 

  18. Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323. https://doi.org/10.1186/1471-2105-12-323

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  19. Robinson J, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, & Mesirov JP (2011) Integrative genomics viewer. Nature Biotechnology, 29(1):24–26

    Google Scholar 

  20. Huang BQ, Sheridan WF (1994) Female gametophyte development in maize: microtubular organization and embryo sac polarity. Plant Cell 6(6):845–861

    CrossRef  PubMed  PubMed Central  Google Scholar 

  21. Tattersall EAR, Ergul A, AlKayal F, DeLuc L, Cushman JC, Cramer GR (2005) A comparison of methods for isolating high-quality RNA from leaves of grapevine. Am J Enol Vitic 56(4):400–406

    CAS  Google Scholar 

  22. Townsley BT, Covington MF, Ichihashi Y, Zumstein K, Sinha NR (2015) BrAD-seq: breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction. Front Plant Sci 6:366. https://doi.org/10.3389/fpls.2015.00366

    CrossRef  PubMed  PubMed Central  Google Scholar 

  23. Ulitsky I (2016) Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nat Rev Genetics 17(10):601–614. https://doi.org/10.1038/nrg.2016.85

    CrossRef  CAS  PubMed  Google Scholar 

  24. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115

    CrossRef  CAS  PubMed  Google Scholar 

Download references

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).

Author information

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

Authors
  1. Linqian Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lin Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gary J. Muehlbauer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. John E. Fowler
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Matthew M. S. Evans
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Matthew M. S. Evans .

Editor information

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

Rights and permissions

Reprints and Permissions

Copyright information

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

About this protocol

Cite this protocol

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

Download citation

  • 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