CO-FISH, COD-FISH, ReD-FISH, SKY-FISH
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Fluorescence in situ hybridization (FISH) has become a powerful tool for exploring genomes at the level of chromosomes. The procedure can be used to identify individual chromosomes, rearrangements between chromosomes, and the location within a chromosome of specific DNA sequences such as centromeres, telomeres, and even individual genes. Chromosome orientation FISH (CO-FISH) extends the information obtainable from standard FISH to include the relative orientation of two or more DNA sequences within a chromosome (Goodwin and Meyne, Cytogenet Cell Genet 63:126–127, 1993). In combination with a suitable reference probe, CO-FISH can also determine the absolute 5′–3′ direction of a DNA sequence relative to the short arm (pter) to long arm (qter) axis of the chromosome. This variation of CO-FISH was originally termed “COD-FISH” (Chromosome orientation and direction FISH) to reflect this fact (Meyne and Goodwin, Chromosome Research 3:375–378, 1995). Telomeric DNA serves as a convenient and absolute reference probe for this purpose, since all G-rich 5′-(TTAGGG) n -3′ telomeric sequences are terminally located and oriented away from the centromere.
In the beginning, CO-FISH was used to detect obligate chromosomal inversions associated with isochromosome formation (Bailey et al., Mutagenesis 11:139–144, 1996), various pericentric inversions (Bailey et al., Cytogenetics and Cell Genetics 75:248–253, 1996), and to confirm the origin of centromeric lateral asymmetry (Goodwin et al., Chromosoma 104:345–347, 1996). More recent and sophisticated applications of CO-FISH include distinction between telomeres produced via leading- vs. lagging-strand DNA synthesis (Bailey et al., Science 293:2462–2465, 2001), identification of interstitial blocks of telomere sequence that result from inappropriate fusion to double-strand breaks (telomere–DSB fusion) (Bailey et al., DNA Repair (Amst) 3:349–357, 2004), discovery of elevated rates of mitotic recombination at chromosomal termini (Cornforth and Eberle, Mutagenesis, 16:85–89, 2001) and sister chromatid exchange within telomeric DNA (T-SCE) (Bailey et al., Nucleic Acids Res 32:3743–3751, 2004), establishing replication timing of mammalian telomeres throughout S-phase (ReD-FISH) (Cornforth et al., In: Cold Spring Harbor Symposium: Telomeres and Telomerase, Cold Spring Harbor, NY, 2003; Zou et al., Proc Natl Acad Sci USA 101:12928–12933, 2004) and in combination with �spectral karyotyping (SKY-CO-FISH) (Williams et al., Cancer Res 69:2100–2107, 2009). For more information, the reader is referred to several reviews (Bailey et al., Cytogenet Genome Res 107, 14–17, 2004; Bailey and Cornforth, Cell Mol Life Sci 64:2956–2964, 2007; Bailey, Telomeres and Double-Strand Breaks – All’s Well that “Ends” Well, Radiat Res 169:1–7, 2008).
