Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

  • Arturo V. OrjaloJr.
  • Hans E. JohanssonEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1402)


RNA fluorescence in situ hybridization (FISH), long an indispensable tool for the detection and localization of RNA, is becoming an increasingly important complement to other gene expression analysis methods. Especially important for long noncoding RNAs (lncRNAs), RNA FISH adds the ability to distinguish between primary and mature lncRNA transcripts and thus to segregate the site of synthesis from the site of action.

We detail a streamlined RNA FISH protocol for the simultaneous imaging of multiple primary and mature mRNA and lncRNA gene products and RNA variants in fixed mammalian cells. The technique makes use of fluorescently pre-labeled, short DNA oligonucleotides (circa 20 nucleotides in length), pooled into sets of up to 48 individual probes. The overall binding of multiple oligonucleotides to the same RNA target results in fluorescent signals that reveal clusters of RNAs or single RNA molecules as punctate spots without the need for enzymatic signal amplification. Visualization of these punctate signals, through the use of wide-field fluorescence microscopy, enables the counting of single transcripts down to one copy per cell. Additionally, by using probe sets with spectrally distinct fluorophores, multiplex analysis of gene-specific RNAs, or RNA variants, can be achieved. The presented examples illustrate how this method can add temporospatial information between the transcription event and both the location and the endurance of the mature lncRNA. We also briefly discuss post-processing of images and spot counting to demonstrate the capabilities of this method for the statistical analysis of RNA molecules per cell. This information can be utilized to determine both overall gene expression levels and cell-to-cell gene expression variation.

Key words

Exon Intron Fluorescence In situ hybridization FISH qPCR Single-molecule detection lncRNA mRNA Gene expression Transcription burst Nucleus 



We gratefully acknowledge the continual support of Dr. Ron Cook and members of the Stellaris team at LGC Biosearch Technologies.

For research use only. Not for use in diagnostic procedures. Stellaris® is a trademark of LGC Biosearch Technologies. Products and technologies appearing in this application note may have trademark or patent restrictions associated with them. Please see for a full legal disclosure.


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Research and DevelopmentLGC Biosearch TechnologiesPetalumaUSA
  2. 2.Biological Technologies, Analytical Development & Quality ControlGenentech, Inc.South San FranciscoUSA

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