Detection of MicroRNAs by In Situ Hybridization in Skin

  • Maximilian E. Pickup
  • Mohammed I. AhmedEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2154)


MicroRNAs (miRNAs) are a family of small noncoding RNAs (~19–24 nt) playing a key role in the execution of gene expression programs in various cells and tissues. Many technical challenges have been encountered when investigating miRNAs, in particular, determining the spatiotemporal expression pattern of miRNAs in cells and tissues. We describe here a well-established in situ hybridization protocol for the detection and analysis of spatiotemporal expression patterns of miRNAs in skin and its appendages such as the hair follicle in both frozen and paraffin-embedded tissue sections. We describe in detail the different steps that are associated with utilizing in situ hybridization procedure on either frozen or paraffin-embedded tissues for miRNAs localization. Postfixation, tissues are hybridized with LNA double labeled probes with digoxygenin. Detection of hybridized probes is performed by using an alkaline phosphatase coupled antibody against digoxygenin. The final step involves the use of substrates to develop the color of alkaline phosphatase-LNA-probe structure leading to identification of the spatiotemporal location of target miRNAs in target tissue and cells. We also discuss two options for substrate color development in these procedures: (1) NBT/BCIP and (2) BM Purple. This method is a simple and convenient way of determining the spatiotemporal expression pattern of miRNAs, which has been a challenge since their discovery, due to their relatively small size. Knowledge gained from in situ hybridization is crucial for better understanding of the roles of individual miRNA(s) during distinct stages of development in various cells and tissues. These protocols will be beneficial to the wider scientific community.

Key words

In situ hybridization MicroRNAs Skin and hair follicles 



I would like to thank my mentors Dr. Natalia Botchkareva and Dr. Andrei Mardaryev for their help and support when first introducing in situ hybridization to me as young Ph.D. student. This technique has been crucial for us to understand and delineate the role of microRNAs in skin.


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© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.School of Science and TechnologyNottingham Trent UniversityNottinghamUK

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