Simultaneous isotopic and nonisotopic in situ hybridization histochemistry with cRNA probes

In situ hybridization histochemistry is widely used to study gene expression at the mRNA level in tissues and cells. Double label in situ hybridization allows for coexpression studies. We describe a protocol for the simultaneous hybridization of two cRNA probes tagged with and digoxigenin-UTP, respectively, to frozen brain tissue sections. Hybridization signals of digoxigenin-tagged probes appear as purple cytoplasmic staining following detection of digoxigenin residues by an alkaline-phosphatase-(AP)-linked antibody. Signals resulting from hybridization of radiolabeled probes are detected as silver grains overlying cellular profiles in sections coated with autoradiographic emulsion. Grain counting allows for semiquantitatively estimates of the cellular expression levels of transcripts. Suitable cRNA-probes can be derived from linear templates generated by polymerase chain reaction (PCR) using nested primers which contain RNA-polymerase promotor sites. The cRNA-probes are sensitive and allow an application of this protocol to the detection of a wide range of mRNAs of medium or low abundance.