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MicroRNA In Situ Hybridization

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Next-Generation MicroRNA Expression Profiling Technology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 822))

Abstract

In situ hybridization (ISH) is a technology that allows detection of specific nucleic acid sequences in tissue samples at the cellular level. For detection of individual microRNAs (miRNAs) and mRNAs, the ISH technology determines the cellular origin of expression and provides information on expression levels in different tissue compartments and cell populations. This histological expression analysis is of crucial importance for elucidating roles particularly of miRNAs in molecular and biological processes. mRNA expression analyses can partly be replaced by immunohistochemical detection of the protein encoded by the mRNA. Combined with the short sequences of the miRNAs (18–22 bp), this leaves miRNA ISH as an indispensable yet challenging technology in terms of detection and specificity analysis. In this chapter, a simple miRNA ISH protocol using chromogenic detection is presented. I touch upon critical steps in the ISH protocol, different applications on ISH technology platforms, advantageous use of locked nucleic acids (LNA™) in miRNA detection probes, qualification of clinical paraffin samples, and specificity analyses and quantification of the ISH signal.

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Acknowledgments

Special thanks to ISH team at Exiqon: Stine Jørgensen, Mette Carlsen Mohr, Tina Bisgaard Sørensen, Marie-Louise Lunn, Adam Baker, and Søren Møller for their dedication and support.

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Authors and Affiliations

  1. Exiqon A/S, Diagnostic Product Development, Vedbæk, Denmark

    Boye Schnack Nielsen

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  1. Boye Schnack Nielsen
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Correspondence to Boye Schnack Nielsen .

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Editors and Affiliations

  1. Illumina, Inc., Towne Centre Drive 9885, San Diego, 92121, California, USA

    Jian-Bing Fan

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Nielsen, B.S. (2012). MicroRNA In Situ Hybridization. In: Fan, JB. (eds) Next-Generation MicroRNA Expression Profiling Technology. Methods in Molecular Biology, vol 822. Humana Press. https://doi.org/10.1007/978-1-61779-427-8_5

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  • DOI: https://doi.org/10.1007/978-1-61779-427-8_5

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-426-1

  • Online ISBN: 978-1-61779-427-8

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