Chromosome Orientation fluorescence in situ hybridization or strand-specific FISH

Methods Mol Biol. 2010;659:173-83. doi: 10.1007/978-1-60761-789-1_12.


Chromosome Orientation FISH (CO-FISH) is a technique that can be used to extend the information obtainable from standard FISH to include the relative orientation of two or more DNA sequences within a chromosome. CO-FISH can determine the absolute 5'-to-3' direction of a DNA sequence relative to the short arm-to-long arm axis of the chromosome, and so was originally termed "COD-FISH" (Chromosome Orientation and Direction FISH). CO-FISH has been employed to detect chromosomal inversions associated with isochromosome formation, various pericentric inversions, and to confirm the origin of lateral asymmetry. More recent and sophisticated applications of CO-FISH include distinction between telomeres produced via leading- vs. lagging-strand DNA synthesis, identification of interstitial blocks of telomere sequence that result from inappropriate fusion to double-strand breaks (telomere-DSB fusion), discovery of elevated rates of mitotic recombination at chromosomal termini and sister chromatid exchange within telomeric DNA (T-SCE), establishing replication timing of mammalian telomeres throughout S-phase (ReD-FISH) and to identify chromosomes, in combination with spectral karyotyping (SKY-CO-FISH).

MeSH terms

  • Animals
  • Base Sequence
  • Bromodeoxyuridine / metabolism
  • Chromosomes / metabolism*
  • DNA Probes / genetics
  • DNA Probes / metabolism
  • DNA, Single-Stranded / genetics
  • DNA, Single-Stranded / metabolism
  • Fibroblasts / cytology
  • Fibroblasts / metabolism
  • Humans
  • In Situ Hybridization, Fluorescence / methods*
  • Mice
  • Nucleic Acid Denaturation
  • Peptide Nucleic Acids / genetics
  • Peptide Nucleic Acids / metabolism
  • Telomere / genetics


  • DNA Probes
  • DNA, Single-Stranded
  • Peptide Nucleic Acids
  • Bromodeoxyuridine