Towards quantitative in situ hybridization

J Histochem Cytochem. 1997 Mar;45(3):413-23. doi: 10.1177/002215549704500309.


In situ hybridization analysis of tissue mRNA concentrations remains to be accepted as a quantitative technique, even though exposure of tissue sections to photographic emulsion is equivalent to Northern blot analysis. Because of the biological importance of in situ quantification of RNA sequences within a morphological context, we evaluated the quantitative aspects of this technique. In calibrated microscopic samples, autoradiographic signal (density of silver grains) was proportionate to the radioactivity present, to the exposure time, and to time of development of the photographic emulsion. Similar results were obtained with tissue sections, showing that all steps of the in situ hybridization protocol, before and including the detection of the signal, can be reproducibly performed. Furthermore, the integrated density of silver grains produced in liver and intestinal sections by the in situ hybridization procedure using 35S-labeled riboprobes is directly proportionate to the signal obtained by quantitative Northern blot analysis. The significance of this finding is that in situ quantification of RNA can be realized with high sensitivity and with the additional advantage of the possibility of localizing mRNA within the cells of interest. Application of this procedure on fetal and adult intestinal tissue showed that the carbamoylphosphate synthetase (CPS)-expressing epithelial cells of both tissues accumulated CPS mRNA to the same level but that whole-organ CPS mRNA levels decreased four-to fivefold in the same period, owing to a comparable decrease in the number of CPS-expressing cells in total intestinal tissue.

MeSH terms

  • Animals
  • Autoradiography
  • Blotting, Northern
  • Calibration
  • Carbon-Nitrogen Ligases*
  • Evaluation Studies as Topic
  • Gelatin / analysis
  • Image Processing, Computer-Assisted
  • In Situ Hybridization / methods*
  • Intestines / chemistry
  • Intestines / embryology
  • Ligases / analysis
  • Ligases / genetics
  • Lighting
  • Liver / chemistry
  • Liver / embryology
  • RNA, Messenger / analysis
  • Rats
  • Rats, Wistar
  • Reproducibility of Results


  • RNA, Messenger
  • Gelatin
  • Ligases
  • Carbon-Nitrogen Ligases
  • carbamoyl-phosphate synthetase (N-acetylglutamate)