JoVE Logo
Faculty Resource Center

Sign In




Representative Results






Whole Mount RNA Fluorescent in situ Hybridization of Drosophila Embryos

Published: January 30th, 2013



1Institut de Recherches Cliniques de Montréal (IRCM), 2Department of Biochemistry, Université de Montréal
* These authors contributed equally

Here we describe a whole-mount fluorescent in situ hybridization (FISH) protocol for determining the expression and localization properties of RNAs expressed during embryogenesis in the fruit fly, Drosophila melanogaster.

Assessing the expression pattern of a gene, as well as the subcellular localization properties of its transcribed RNA, are key features for understanding its biological function during development. RNA in situ hybridization (RNA-ISH) is a powerful method used for visualizing RNA distribution properties, be it at the organismal, cellular or subcellular levels 1. RNA-ISH is based on the hybridization of a labeled nucleic acid probe (e.g. antisense RNA, oligonucleotides) complementary to the sequence of an mRNA or a non-coding RNA target of interest 2. As the procedure requires primary sequence information alone to generate sequence-specific probes, it can be universally applied to a broad range of organisms and tissue specimens 3. Indeed, a number of large-scale ISH studies have been implemented to document gene expression and RNA localization dynamics in various model organisms, which has led to the establishment of important community resources 4-11. While a variety of probe labeling and detection strategies have been developed over the years, the combined usage of fluorescently-labeled detection reagents and enzymatic signal amplification steps offer significant enhancements in the sensitivity and resolution of the procedure 12. Here, we describe an optimized fluorescent in situ hybridization method (FISH) employing tyramide signal amplification (TSA) to visualize RNA expression and localization dynamics in staged Drosophila embryos. The procedure is carried out in 96-well PCR plate format, which greatly facilitates the simultaneous processing of large numbers of samples.

1. RNA Probe Preparation

Overview: The following section describes the steps required to make Digoxigenin (Dig)-labeled RNA probes suitable for FISH. The first step involves cloning or PCR amplifying a sequence corresponding to the transcribed region of a gene of interest that will be used to generate a sequence-specific probe. This can be achieved by first cloning the gene segment into a plasmid in which the multiple cloning site is flanked by bacteriophage promoter elements (T.......

Log in or to access full content. Learn more about your institution’s access to JoVE content here

When performed successfully, this procedure offers a strikingly enhanced level of detail in the spatio-temporal analysis of gene expression and mRNA localization dynamics during early Drosophila embryogenesis. Indeed, as illustrated in Figure 3A for the classical pair-rule gene runt (run), one can use this protocol to observe gene expression events via the detection of nascent transcript foci in groups of expressing nuclei. In addition, as shown in the embryo mosaic in

Log in or to access full content. Learn more about your institution’s access to JoVE content here

For probe synthesis steps, we typically generate run-off antisense RNA probes by in vitro transcription from full-length Drosophila cDNAs amplified from plasmids found in the Drosophila Gene Collection (DGC), a resource detailed at the following website: 14,15. This approach has been used extensively in large scale ISH studies aimed at mapping gene expression and mRNA localizat.......

Log in or to access full content. Learn more about your institution’s access to JoVE content here

Work conducted in the Lécuyer laboratory is supported by funding from the National Sciences and Engineering Council of Canada (NSERC), the Canadian Institutes of Health Research (CIHR) and the Fonds de Recherche en Santé du Québec (FRSQ). Fabio Alexis Lefebvre and Gaël Moquin-Beaudry are supported by NSERC undergraduate research studentships, while Carole Iampietro is supported by the Angelo Pizzagalli postdoctoral fellowship.


Log in or to access full content. Learn more about your institution’s access to JoVE content here

Name Company Catalog Number Comments
Name of the Reagent Company Catalogue Number Comments (optional)
T7, T3 or SP6 RNA Polymerase Fermentas Life Sciences EP0101,EP0111,EP0131 Kits contain reaction buffer.
DIG RNA Labeling Mix Roche Applied Science 11 277 073 910
RNAguard Amersham Biosciences 27-0816-01
3M sodium acetate
Cold 100% ethanol.
Cold 70% ethanol.
Chlorine bleach solution diluted 1:1 with water.
proteinase K Sigma Aldrich Oakville, ON, Canada Catalog No. P2308
40% formaldehyde solution, freshly prepared
PBS-Tween solution (PBT) 1xPBS, 0.1% Tween-20
Glycine solution 2 mg/ ml glycine in PBT
HRP-conjugated mouse monoclonal anti-DIG Jackson ImmunoResearch Laboratories Inc 200-032- 156 (1/400 dilution of a 1 mg/ml stock solution in PBTB
HRP-conjugated sheep monoclonal anti-DIG Roche Applied Science, Laval, QC 1 207 733 1/500 dilution of stock solution in PBTB
Biotin-conjugated mouse monoclonal anti-DIG Jackson ImmunoResearch Laboratories Inc., West Grove, PA, USA 200-062-156 (1/400 dilution of a 1 mg/ml stock solution in PBTB
Streptavidin-HRP conjugate Molecular Probes, Eugene OR, USA S991 (1/100 dilution of a 1 μg/ml stock

  1. Wilcox, J. N. Fundamental principles of in situ hybridization. J. Histochem. Cytochem. 41, 1725-1733 (1993).
  2. Tautz, D., Pfeifle, C. A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchback. Chromosoma. 98, 81-85 (1989).
  3. Lecuyer, E., Tomancak, P. Mapping the gene expression universe. Curr Opin Genet Dev. 18, 506-512 (2008).
  4. Tomancak, P., et al. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 8, 2007-208 (2007).
  5. Thisse, B., et al. Spatial and temporal expression of the zebrafish genome by large-scale in situ hybridization screening. Methods Cell Biol. 77, 505-519 (2004).
  6. Quiring, R., et al. Large-scale expression screening by automated whole-mount in situ hybridization. Mech. Dev. 121, 971-976 (2004).
  7. Pollet, N., et al. An atlas of differential gene expression during early Xenopus embryogenesis. Mech. Dev. 122, 365-439 (2005).
  8. Lein, E. S., et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature. 445, 168-176 (2007).
  9. Lecuyer, E., et al. Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell. 131, 174-187 (2007).
  10. Imai, K. S., Levine, M., Satoh, N., Satou, Y. Regulatory blueprint for a chordate embryo. Science. 312, 1183-1187 (2006).
  11. Bell, G. W., Yatskievych, T. A., Antin, P. B. GEISHA, a whole-mount in situ hybridization gene expression screen in chicken embryos. Dev. Dyn. 229, 677-687 (2004).
  12. Wilkie, G. S., Shermoen, A. W., O'Farrell, P. H., Davis, I. Transcribed genes are localized according to chromosomal position within polarized Drosophila embryonic nuclei. Curr. Biol. 9, 1263-1266 (1999).
  13. Rothwell, W. F., Sullivan, W. Drosophila embryo dechorionation. CSH Protoc. , (2007).
  14. Stapleton, M., et al. The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res. 12, 1294-1300 (2002).
  15. Rubin, G. M., et al. A Drosophila complementary DNA resource. Science. 287, 2222-2224 (2000).
  16. Tomancak, P., et al. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 3, (2002).
  17. Terashima, J., Bownes, M. Translating available food into the number of eggs laid by Drosophila melanogaster. Genetics. 167, 1711-1719 (2004).
  18. Lecuyer, E., Parthasarathy, N., Krause, H. M. Fluorescent in situ hybridization protocols in Drosophila embryos and tissues. Methods Mol. Biol. 420, 289-302 (2008).
  19. Lecuyer, E. High resolution fluorescent in situ hybridization in Drosophila. Methods Mol. Biol. 714, 31-47 (2011).
  20. Kosman, D., et al. Multiplex detection of RNA expression in Drosophila embryos. Science. 305, 846 (2004).

This article has been published

Video Coming Soon

JoVE Logo


Terms of Use





Copyright © 2024 MyJoVE Corporation. All rights reserved