In situ detection of precursor and mature microRNAs in paraffin embedded, formalin fixed tissues and cell preparations

Methods. 2008 Jan;44(1):39-46. doi: 10.1016/j.ymeth.2007.10.008.


The in situ detection of microRNAs (miRs) expression offers several challenges. It would be advantageous to have a method which can be used in paraffin embedded, formalin fixed tissue to be able to access the large data bank of archival material. Further, it would be helpful if one could differentiate between precursor and mature, active forms of the miR. In this review, two different methods for the in situ detection of miR in paraffin embedded, formalin fixed tissues are described. Detection of the inactive precursor miR can be accomplished by RT in situ PCR. This will allow the detection of one copy of a given pre-miR per cell. Detection of the mature form of a given miR can be accomplished with in situ hybridization with a labeled probe in which some of the nucleotides have been modified; this is referred to as a locked nucleic acid (LNA) probe. An intense signal after in situ detection with the LNA probe documents marked up-regulation of the, typically, mature miR. Further, one can easily determine the specific subcellular compartmentalization of the precursor and mature forms which may provide insight into the modulation of these important regulatory molecules and their targets.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Fixatives
  • Formaldehyde
  • HL-60 Cells
  • Humans
  • In Situ Hybridization / methods*
  • MicroRNAs / analysis*
  • Paraffin Embedding / methods*
  • Polymerase Chain Reaction / methods*
  • RNA Precursors / analysis*
  • Tissue Fixation / methods*


  • Fixatives
  • MicroRNAs
  • RNA Precursors
  • Formaldehyde