Abstract
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).
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References
Goodwin, E. and Meyne, J. (1993) Strand-specific FISH reveals orientation of chromosome 18 alphoid DNA. Cytogenet Cell Genet, 63, 126–127.
Meyne, J. and Goodwin, E.H. (1995) Direction of DNA-sequences within chromatids determined using strand-specific fish. Chromosome Res, 3, 375–378.
Bailey, S.M., Goodwin, E.H., Meyne, J. and Cornforth, M.N. (1996) CO-FISH reveals inversions associated with isochromosome formation. Mutagenesis, 11, 139–144.
Bailey, S.M., Meyne, J., Cornforth, M.N., McConnell, T.S. and Goodwin, E.H. (1996) A new method for detecting pericentric inversions using COD-FISH. Cytogenet Cell Genet, 75, 248–253.
Goodwin, E.H., Meyne, J., Bailey, S.M. and Quigley, D. (1996) On the origin of lateral asymmetry. Chromosoma, 104, 345–347.
Bailey, S.M., Cornforth, M.N., Kurimasa, A., Chen, D.J. and Goodwin, E.H. (2001) Strand-specific postreplicative processing of mammalian telomeres. Science, 293, 2462–2465.
Bailey, S.M., Cornforth, M.N., Ullrich, R.L. and Goodwin, E.H. (2004) Dysfunctional mammalian telomeres join with DNA double-strand breaks. DNA Repair (Amst), 3, 349–357.
Cornforth, M.N. and Eberle, R.L. (2001) Termini of human chromosomes display elevated rates of mitotic recombination. Mutagenesis, 16(1), 85–89.
Bailey, S.M., Brenneman, M.A. and Goodwin, E.H. (2004) Frequent recombination in telomeric DNA may extend the proliferative life of telomerase-negative cells. Nucleic Acids Res, 32, 3743–3751.
Cornforth, M.N., Eberle, R.L., Loucas, B.D., Fox, M.H. and Bailey, S.M. (2003) Cold Spring Harbor Symposium: Telomeres and Telomerase, Cold Spring Harbor, NY.
Zou, Y., Gryaznov, S.M., Shay, J.W., Wright, W.E. and Cornforth, M.N. (2004) Asynchronous replication timing of telomeres at opposite arms of mammalian chromosomes. Proc Natl Acad Sci U S A, 101, 12928–12933.
Williams, E.S., Klingler, R., Ponnaiya, B., Hardt, T., Schrock, E., Lees-Miller, S.P., Meek, K., Ullrich, R.L. and Bailey, S.M. (2009) Telomere dysfunction and DNA-PKcs deficiency: characterization and consequence. Cancer Res, 69, 2100–2107
Bailey, S.M., Goodwin, E.H. and Cornforth, M.N. (2004) Strand-specific fluorescence in situ hybridization: the CO-FISH family. Cytogenet Genome Res, 107, 14–17.
Bailey, S.M. and Cornforth, M.N. (2007) Telomeres and DNA double-strand breaks: ever the twain shall meet? Cell Mol Life Sci, 64, 2956–2964
Bailey, S.M. (2008) Telomeres and double-strand breaks – All’s well that “Ends” well. Radiat Res, 169, 1–7.
Bechter, O.E., Zou, Y., Walker, W., Wright, W.E. and Shay, J.W. (2004) Telomeric recombination in mismatch repair deficient human colon cancer cells after telomerase inhibition. Cancer Res, 64, 3444–3451.
Londono-Vallejo, J.A., Der-Sarkissian, H., Cazes, L., Bacchetti, S. and Reddel, R.R. (2004) Alternative lengthening of telomeres is characterized by high rates of telomeric exchange. Cancer Res, 64, 2324–2327.
Blagoev, K.B. and Goodwin, E.H. (2008) Telomere exchange and asymmetric segregation of chromosomes can account for the unlimited proliferative potential of ALT cell populations. DNA Repair (Amst), 7, 199–204.
Hayata, I. (1993) Removal of stainable cytoplasmic substances from cytogenetic slide preparations. Biotechnic & Histochemistry, 68, 150–152.
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Bailey, S.M., Williams, E.S., Cornforth, M.N., Goodwin, E.H. (2010). Chromosome Orientation Fluorescence In Situ Hybridization or Strand-Specific FISH. In: Bridger, J., Volpi, E. (eds) Fluorescence in situ Hybridization (FISH). Methods in Molecular Biology, vol 659. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-789-1_12
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DOI: https://doi.org/10.1007/978-1-60761-789-1_12
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