Rapid in situ codetection of noncoding RNAs and proteins in cells and formalin-fixed paraffin-embedded tissue sections without protease treatment

Nat Protoc. 2010 Jun;5(6):1061-73. doi: 10.1038/nprot.2010.62. Epub 2010 May 20.


Noncoding RNAs (ncRNAs) comprise a diverse group of RNAs that function in essential cellular processes such as pre-mRNA splicing and mRNA translation and also regulate various aspects of gene expression in physiology and development. Methods of subcellular and tissue localization of ncRNAs are essential to understand their biological roles and their contribution to disease. We describe a rapid fluorescent (FISH) or chromogenic (CISH) in situ hybridization protocol for localization of ncRNAs (including microRNAs (miRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), piwi-associated RNAs (piRNAs) and ribosomal RNAs (rRNAs)) in formalin-fixed, paraffin-embedded (FFPE) tissues and cultured cells, using locked nucleic acid (LNA)-modified oligonucleotides. In this protocol, sections are heated in citrate buffer, which eliminates the need for protease treatment, thus preserving optimal morphology and protein epitopes, and allowing the simultaneous detection of proteins with immunofluorescence staining (IF). LNA-FISH requires 5 h, or between 10 and 36 h when combined with IF; LNA-CISH requires 2 d.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Sequence
  • Cells, Cultured
  • DNA Probes / genetics
  • Fluorescent Antibody Technique
  • Formaldehyde
  • HeLa Cells
  • Humans
  • In Situ Hybridization, Fluorescence / methods*
  • Paraffin Embedding
  • Proteins / metabolism*
  • RNA, Untranslated / genetics*
  • RNA, Untranslated / metabolism*
  • Tissue Fixation


  • DNA Probes
  • Proteins
  • RNA, Untranslated
  • Formaldehyde