Int. J. Mol. Sci. 2015, 16, 13259-13286; doi:10.3390/ijms160613259 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Review Small RNA Detection by in Situ Hybridization Methods Martyna O. Urbanek †, Anna U. Nawrocka † and Wlodzimierz J. Krzyzosiak * Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland; E-Mails:
[email protected] (M.O.U.);
[email protected] (A.U.N.) † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail:
[email protected]; Tel.: +48-61-852-8503; Fax: +48-61-852-0532. Academic Editor: Michael Ladomery Received: 29 April 2015 / Accepted: 3 June 2015 / Published: 10 June 2015 Abstract: Small noncoding RNAs perform multiple regulatory functions in cells, and their exogenous mimics are widely used in research and experimental therapies to interfere with target gene expression. MicroRNAs (miRNAs) are the most thoroughly investigated representatives of the small RNA family, which includes short interfering RNAs (siRNAs), PIWI-associated RNA (piRNAs), and others. Numerous methods have been adopted for the detection and characterization of small RNAs, which is challenging due to their short length and low level of expression. These include molecular biology methods such as real-time RT-PCR, northern blotting, hybridization to microarrays, cloning and sequencing, as well as single cell miRNA detection by microscopy with in situ hybridization (ISH). In this review, we focus on the ISH method, including its fluorescent version (FISH), and we present recent methodological advances that facilitated its successful adaptation for small RNA detection.