Identification of Long Noncoding RNAs in the Developing Endosperm of Maize

  • Eundeok Kim
  • Yuqing Xiong
  • Byung-Ho Kang
  • Sibum SungEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1933)


Maize endosperm consists of three distinct types of tissues, including the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Compartmentalization of these tissues during endosperm differentiation makes the endosperm development an excellent model to study changes in gene expression during development. By utilizing cryo-dissection of developing endosperm, morphologically distinct samples can be obtained for transcriptome and epigenome analysis. Here, we describe methods for the isolation of tissues from developing maize endosperm and for the transcriptome analysis to identify novel long noncoding RNAs. The transcriptome data can be further analyzed to illustrate spatiotemporal changes in both coding and noncoding transcripts during the endosperm development.

Key words

Endosperm Long noncoding RNAs Transcriptome analysis Cryo-dissection Maize In situ hybridization 



B.H. Kang and S. Sung are supported by USDA NIFA Award AFRI grant (2011-67013-30119). B.H. Kang is also supported by the grants from the Research Grants Council (RGC) of Hong Kong (GRF14126116, C4011-14R, and AoE/M-05/12), Cooperative Research Program for Agriculture Science and Technology Development (Project No. 10953092018), and Rural Development Administration, Republic of Korea, and S. Sung is also supported by NIH (GM100108) and NSF (1656764).

Supplementary material

978-1-4939-9045-0_3_MOESM1_ESM.docx (40 kb)
Supplementary File 1. Python script used for filtering small RNAs X (DOCX 40 kb)
978-1-4939-9045-0_3_MOESM2_ESM.docx (21 kb)
Supplementary File 2. Python script used for filtering transcripts from transposable elements X (DOCX 20 kb)


  1. 1.
    Fatica A, Bozzoni I (2014) Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet 15(1):7–21. Scholar
  2. 2.
    Kim DH, Sung S (2017) Vernalization-triggered intragenic chromatin loop formation by long noncoding RNAs. Dev Cell 40(3):302–312 e304. Scholar
  3. 3.
    Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331(6013):76–79. Scholar
  4. 4.
    Quinn JJ, Chang HY (2016) Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet 17(1):47–62. Scholar
  5. 5.
    Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY (2015) Systematic discovery of Xist RNA binding proteins. Cell 161(2):404–416. Scholar
  6. 6.
    Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigo R (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775–1789. Scholar
  7. 7.
    Rutenberg-Schoenberg M, Sexton AN, Simon MD (2016) The properties of long noncoding RNAs that regulate chromatin. Annu Rev Genomics Hum Genet 17:69–94. Scholar
  8. 8.
    Goff LA, Rinn JL (2015) Linking RNA biology to lncRNAs. Genome Res 25(10):1456–1465. Scholar
  9. 9.
    Zhang S, Thakare D, Yadegari R (2018) Laser-capture microdissection of maize kernel compartments for RNA-Seq-based expression analysis. Methods Mol Biol 1676:153–163. Scholar
  10. 10.
    Kim ED, Xiong Y, Pyo Y, Kim DH, Kang BH, Sung S (2017) Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development. Sci Rep 7(1):3838. Scholar
  11. 11.
    Kiyota E, Pena IA, Arruda P (2015) The saccharopine pathway in seed development and stress response of maize. Plant Cell Environ. Scholar
  12. 12.
    Zhang Z, Yang J, Wu Y (2015) Transcriptional regulation of zein gene expression in maize through the additive and synergistic action of opaque2, prolamine-box binding factor, and O2 heterodimerizing proteins. Plant Cell 27(4):1162–1172. Scholar
  13. 13.
    Zhan J, Thakare D, Ma C, Lloyd A, Nixon NM, Arakaki AM, Burnett WJ, Logan KO, Wang D, Wang X, Drews GN, Yadegari R (2015) RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation. Plant Cell 27(3):513–531. Scholar
  14. 14.
    Zhang W, Yan H, Chen W, Liu J, Jiang C, Jiang H, Zhu S, Cheng B (2014) Genome-wide identification and characterization of maize expansion genes expressed in endosperm. Mol Genet Genomics 289(6):1061–1074. Scholar
  15. 15.
    Xiong Y, Mei W, Kim ED, Mukherjee K, Hassanein H, Barbazuk WB, Sung S, Kolaczkowski B, Kang BH (2014) Adaptive expansion of the maize maternally expressed gene (Meg) family involves changes in expression patterns and protein secondary structures of its members. BMC Plant Biol 14:204. Scholar
  16. 16.
    Xiong YQ, Li QB, Kang BH, Chourey PS (2011) Discovery of genes expressed in basal endosperm transfer cells in maize using 454 transcriptome sequencing. Plant Molecular Biology Reporter 29(4):835–847. Scholar
  17. 17.
    Boerner S, McGinnis KM (2012) Computational identification and functional predictions of long noncoding RNA in Zea mays. PLoS One 7(8):e43047. PONE-D-12-12079 [pii].CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28–36PubMedPubMedCentralGoogle Scholar
  19. 19.
    Gupta M (2007) Generalized hierarchical markov models for the discovery of length-constrained sequence features from genome tiling arrays. Biometrics 63(3):797–805. Scholar

Copyright information

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

Authors and Affiliations

  • Eundeok Kim
    • 1
    • 2
  • Yuqing Xiong
    • 3
  • Byung-Ho Kang
    • 3
    • 4
  • Sibum Sung
    • 1
    • 5
    Email author
  1. 1.Department of Molecular Biosciences and Institute for Cellular and Molecular BiologyThe University of Texas at AustinAustinUSA
  2. 2.Department of BiologyUniversity of WashingtonSeattleUSA
  3. 3.Microbiology and Cell ScienceUniversity of FloridaGainesvilleUSA
  4. 4.School of Life Sciences, State Key Laboratory for AgrobiotechnologyThe Chinese University of Hong KongShatinChina
  5. 5.International Scholar, Kyung-Hee UniversitySuwonSouth Korea

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