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In Situ Detection of Mature miRNAs in Plants Using LNA-Modified DNA Probes

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RNA Abundance Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 883))

Abstract

MicroRNAs (miRNAs) play important roles in development in plants, and some miRNAs show developmentally regulated organ- and tissue-specific expression patterns. Therefore, in situ detection of mature miRNAs is important for understanding the functions of both miRNAs and their targets. The construction of promoter–reporter fusions and examination of their in planta expression have been widely used and the results obtained thus far are rather informative; however, in some cases, the length of promoter that contains the entire regulatory elements is difficult to determine. In addition, traditional in situ hybridization with the antisense RNA fragment as the probe usually fails to detect miRNAs because the mature miRNAs are too short (∼21 nt) to exhibit stable hybridization signals. In recent years, the locked nucleic acid (LNA)-modified DNA probe has been successfully used in animals and plants to detect small RNAs. Here, we describe a modified protocol using LNA-modified DNA probes to detect mature miRNAs in plant ­tissues, including the design of LNA probes and detailed steps for the in situ hybridization experiment, using Arabidopsis miR165 as an example.

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Acknowledgments

We are grateful to H. Wang for discussion with the manuscript. We thank Dr. Y. Eshed and Dr. I. Pekker for sharing experience on LNA probes. This work was supported by grants from the Chief Scientist Program of Shanghai Institutes for Biological Sciences, the Chinese National Scientific Foundation 30630041, and Chinese Academy of Sciences (KSCX2-YW-N-057).

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Authors and Affiliations

  1. National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

    Xiaozhen Yao, Hai Huang & Lin Xu

Authors
  1. Xiaozhen Yao
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  2. Hai Huang
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  3. Lin Xu
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Corresponding author

Correspondence to Lin Xu .

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Editors and Affiliations

  1. , Dept. Plant Pathology & Microbiology, University of California, University Avenue 900, Riverside, 92521, USA

    Hailing Jin

  2. , Division of Plant Sciences, University of Missouri, Agriculture Building 1-31, Columbia, 65211, Missouri, USA

    Walter Gassmann

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Yao, X., Huang, H., Xu, L. (2012). In Situ Detection of Mature miRNAs in Plants Using LNA-Modified DNA Probes. In: Jin, H., Gassmann, W. (eds) RNA Abundance Analysis. Methods in Molecular Biology, vol 883. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-839-9_11

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  • DOI: https://doi.org/10.1007/978-1-61779-839-9_11

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-838-2

  • Online ISBN: 978-1-61779-839-9

  • eBook Packages: Springer Protocols

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