CO-FISH, COD-FISH, ReD-FISH, SKY-FISH.

Eli S. Williams, Michael Cornforth, Edwin H. Goodwin, Susan M. Bailey

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

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).

Original languageEnglish (US)
Pages (from-to)113-124
Number of pages12
JournalMethods in molecular biology (Clifton, N.J.)
Volume735
DOIs
StatePublished - 2011
Externally publishedYes

Fingerprint

Fluorescence In Situ Hybridization
Chromosomes
Telomere
Centromere
Mutagenesis
Spectral Karyotyping
Isochromosomes
Genome
Viverridae
Sister Chromatid Exchange
Chromosomes, Human, Pair 3
Telomerase
DNA
S Phase
Cytogenetics
DNA Repair
Nucleic Acids
Genetic Recombination

ASJC Scopus subject areas

  • Medicine(all)

Cite this

CO-FISH, COD-FISH, ReD-FISH, SKY-FISH. / Williams, Eli S.; Cornforth, Michael; Goodwin, Edwin H.; Bailey, Susan M.

In: Methods in molecular biology (Clifton, N.J.), Vol. 735, 2011, p. 113-124.

Research output: Contribution to journalArticle

Williams, Eli S. ; Cornforth, Michael ; Goodwin, Edwin H. ; Bailey, Susan M. / CO-FISH, COD-FISH, ReD-FISH, SKY-FISH. In: Methods in molecular biology (Clifton, N.J.). 2011 ; Vol. 735. pp. 113-124.
@article{76029b65455d44a199f5b18a330cdbeb,
title = "CO-FISH, COD-FISH, ReD-FISH, SKY-FISH.",
abstract = "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).",
author = "Williams, {Eli S.} and Michael Cornforth and Goodwin, {Edwin H.} and Bailey, {Susan M.}",
year = "2011",
doi = "10.1007/978-1-61779-092-8_11",
language = "English (US)",
volume = "735",
pages = "113--124",
journal = "Methods in Molecular Biology",
issn = "1064-3745",
publisher = "Humana Press",

}

TY - JOUR

T1 - CO-FISH, COD-FISH, ReD-FISH, SKY-FISH.

AU - Williams, Eli S.

AU - Cornforth, Michael

AU - Goodwin, Edwin H.

AU - Bailey, Susan M.

PY - 2011

Y1 - 2011

N2 - 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).

AB - 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).

UR - http://www.scopus.com/inward/record.url?scp=79961011778&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79961011778&partnerID=8YFLogxK

U2 - 10.1007/978-1-61779-092-8_11

DO - 10.1007/978-1-61779-092-8_11

M3 - Article

VL - 735

SP - 113

EP - 124

JO - Methods in Molecular Biology

JF - Methods in Molecular Biology

SN - 1064-3745

ER -