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Preparation of extended DNA fibres for high resolution mapping by fluorescence in situ hybridization (FISH)

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Plant Molecular Biology Manual

Abstract

One of the objectives in genome research is the integration of genetic, molecular and cytogenetic maps. A major step towards the realization of this challenging goal involves the localization of the physical positions of DNA sequences within an entire set of chromosomes by fluorescence in situ hybridization (FISH). This technique permits the identification of entire genomes, individual chromosomes, subchromosomal regions and single copy genes and is, therefore, a highly versatile tool in studying a variety of genomic issues, e.g. interspecific hybrids, chromosome rearrangements, distribution of repetitive DNA sequences and gene mapping.

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References

  1. Austin RH, Brody JP, Cox EC, Duke T and Volkmuth W (1997) Stretch genes. Physics today, Februari issue: 32–38

    Google Scholar 

  2. Brayward P, Menninger J, Lieman J, Desai T, Mokady N, Banks A and Ward DC (1996) Integration of the cytogenetic, genetic and physical maps of the human genome by fish mapping of ceph yac clones. Genomics 32: 1–14

    Article  Google Scholar 

  3. Cai W, Aburatani H, Stanton VP Jr, Housman DE, Wang Y-K and Schwartz DC (1995) Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces. Proc Natl Acad Sci USA 92: 5164–5168

    Article  Google Scholar 

  4. Dauwerse JG, Wiegant J, Raap AK, Breuning MH, and van Ommen GJ (1992) Multiple colors by fluorescence in situ hybridization using ratio-labelled DNA probes create a molecular karyotype. Hum. Mol. Genet. 1:593–598.

    Article  Google Scholar 

  5. Fan Y-S, Davis LM and Shows TB (1990) Mapping of small sequences by fluorescence in situ hybridization directly on banded metaphase chromosomes. Proc. Natl. Acad. Sci. USA 87: 6223–6227.

    Article  Google Scholar 

  6. Fantes J, Redeker B, Breen M, Boyle S, Brown J, Fletcher J, Jones S, Bickmore W, Fukushima Y, Mannens M, Danes S, van Heyningen V and Hanson I (1995) Aninridia-associated cytogenetic rearrangements suggest that a position effect may cause the mutant fenotype. Hum. Molec. Genet. 4: 415–422

    Article  Google Scholar 

  7. Fidlerová H, Senger G, Kost M, Sanséau P and Sheer D. (1994) Two simple procedures for releasing chromatin from routinely fixed cells for fluorescence in situ hybrization. Cytogenet Cell Genet 65: 203–205.

    Article  Google Scholar 

  8. Florijn RJ, LAJ Bonden, Vrolijk H, Wiegant J, Vaandrager J-W, Baas F, den Dunne, JT, Tanke HJ, van Ommen G-JB and Raap AK (1995) High resolution DNA mapping and colour bar-coding of large genes. Human Mol. Genet. 4: 831–836.

    Article  Google Scholar 

  9. Foe VE, Wilkinson LE and Laird CD (1976) Comparative organization of active tramscription units in Oncopeltus fasciatus. Cell 9:131–146

    Article  Google Scholar 

  10. Fransz PF, Alonso-Blanco C, Liharska T, Peeters AJM, Zabel P and De Jong JH (1996) High resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres Plant J. 9: 421–430

    Article  Google Scholar 

  11. Fransz PF, Stam S, Montijn B, Ten Hoopen R, Wiegant J, Kooter JM, Oud O, Nanninga N (1996) Detection of single-copy genes and chromosome rearrangements in Petunia hybrida by fluorescence in situ hybridization Plant J. 9: 767–774

    Article  Google Scholar 

  12. Fransz PF, Armstrong S and Jones GH (1997) A cytogenetic reconstruction of the short arm of chromosome 4 of Arabidopsis thaliana by FISH using repeats, single copy DNA clones and YACs. Physical Mapping of Plant Chromosomes. Aberystwyth Cell Genetic Group 7th Annual Conference, Aberystwyth, p13.

    Google Scholar 

  13. Gerdes MG, Carter MC, Moen JPT, and Lawrence JB (1994) Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos. J. Cell. Biol. 126: 289–304.

    Article  Google Scholar 

  14. Goffeau A, (1997) Molecular fish on chips. Nature 385: 202–203

    Article  Google Scholar 

  15. Haaf T and Ward DC (1994a) Structural analysis of a-satellite DNA and centromere proteins using extended chromatin and chromosomes. Hum Molec Genet 3: 697–709.

    Article  Google Scholar 

  16. Haaf T and Ward DC (1994b) High resolution ordering of YAC contigs using extended chromatin and chromosomes. Hum Molec Genet 3: 629–633.

    Article  Google Scholar 

  17. Heiskanen MR, Karhu R, Hellsten E, Peltonen L, Kallioniemi OP and Palotie A (1994) High resolution mapping using fluorescence in situ hybridisation to extended DNA fibres prepared from agarose embedded cells. BioTechniques 17: 928–933

    Google Scholar 

  18. Heng HHQ, Squire J and Tsui L-C (1992) High resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc. Natl. Acad. Sci. U.S.A. 89: 9509–9513.

    Article  Google Scholar 

  19. Houseal TW, Dackowski WR, Landes GM and Klinger KW (1994) High resolution mapping of overlapping cosmids by fluorescence in situ hybridization. Cytometry 15: 193–198.

    Article  Google Scholar 

  20. Lawrence JB, Villnave CA and Singer RH (1988) Sensitive high-resolution chromatin and chromosome mapping in situ: Presence and oreintation of two closely integrated copies of EBV in a lymphoma line. Cell 52: 51–61.

    Article  Google Scholar 

  21. Liu Y-G and Whittier RF (1994) Rapid preparation of megabase plant DNA from nuclei in agarose plugs and microbeads. Nucl. Acids Res. 22: 2168–2169

    Article  Google Scholar 

  22. Moscone EA, Matze MA and Matzke AJM (1996 ) The use of combined FISH/GISH in conjunction with DAPI counterstaining to identify chromosomes containing transgene inserts in amphidiploid tobacco. Chromosoma 105: 231–236

    Article  Google Scholar 

  23. Moens PB and Pearlman RE (1990) In situ DNA sequence mapping with surface-spread mouse pachytene chromosomes. Cytogenet. Cell Genet. 53:219–220

    Article  Google Scholar 

  24. Miller OL and Beatty BR (1969) Visualization of nucleolar genes. Science 164: 955–957

    Article  Google Scholar 

  25. Parra I and Windle B (1993) High resolution visual mapping of stretched DNA by fluorescent hybridization. Nature Gen 5: 17–21.

    Article  Google Scholar 

  26. Raap AK, Van der Corput MPC, Vervenne RAW, Van Gijlswijk RPM, Tanke HJ and Wiegant J (1995) Ultra-sensitive FISH using peroxidase-mediated deposition of biotin-or fluorochrome tyramides. Hum. Molec. Genet. 4: 529–534

    Article  Google Scholar 

  27. Richard F, Vogt N, Muleris M, Malfoy B, and Dutrillaux B. (1994) Increased FISH efficiency using APC probes generated by direct incorporation of labelled nucleotides by PCR. Cytogenet. Cell Genet. 65: 169–171

    Article  Google Scholar 

  28. Rosenberg C, Florijn RJ, Van De Rijke FM, Blonden LAJ, Raap TK, Van Ommen GJB and Den Dunnen JT (1996) High resolution DNA fibre-FISH on yeast artificial chromosomes: direct visualization of DNA replication. Nature Genetics 10:477–479

    Google Scholar 

  29. Schrock E, du Manoir S, Veldman T, Schoell B, Wienberg J, Ferguson-Smith MA, Ning Y, Ledbetter DH, Bar-Am I, Soenksen S, Garini Y and Ried T (1996) Multicolor spectral karyotyping of human chromosomes. Science 273: 494–497

    Article  Google Scholar 

  30. Senger G, Jones TA, Fidlerová H, Sanséau P, Trowsdale J, Duff M and Sheer D (1994) Released chromatin: linearized DNA for high resolution fluorescence in situ hybridization. Human Molec Genet 3: 1275–1280.

    Article  Google Scholar 

  31. Shen DL, Wang ZF, and Wu M (1987) Gene mapping on maize pachytene chromosomes by in situ hybridization. Chromosoma 95: 311–314.

    Article  Google Scholar 

  32. Speicher MR, Gwyn Ballard S and Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nature Genet. 12: 368–375

    Article  Google Scholar 

  33. Ten Hoopen R, Robbins T, Fransz P, Montijn M, Oud J, Gerats A and Nanninga N (1996) Localization of T-DNA inserts in Petunia by fluorescence in situ hybridization: Physical evidence for suppression of recombination. Plant Cell 8: 823–830

    Google Scholar 

  34. Trask B, Pinkel D and van den Engh G (1989) The proximity of DNA sequences in interphase cell nuclei correlated to genomic distance and permits ordering of cosmids spanning 250 kilobase pairs. Genomics 5: 710–717.

    Article  Google Scholar 

  35. Trask B, Massa H, Kenwrick S. and Gitschier J (1991) Mapping of human chromosome Xq28 by two-color fluorescence in situ hybridization of DNA sequences to interphase cell nuclei. Am J Hum Genet 48: 1–15.

    Google Scholar 

  36. Vogelstein B, Pardoll DM and Coffey DS (1980) Supercoiled loops and eucaryotic DNA replication. Cell 22: 79–85.

    Article  Google Scholar 

  37. Weier H-UG, Wang M, Mullikin JC, Cheng J-F, Greulich KM, Bensimon A and Gray JW (1995) Quantitive DNA fibre mapping. Hum. Molec. Genet. 4: 1903–1910

    Article  Google Scholar 

  38. Wiegant J, Kalle W, Mullenders L, Brookes S, Hoovers JMN, Dauwerse JG, van Ommen GJB and Raap AK (1992) High-resolution in situ hybridization using DNA halo preparations. Hum Molec Genet 1: 587–591.

    Article  Google Scholar 

  39. Xu J and Earle ED (1996) High resolution physical mapping of 45S (5.8S, 18S and 25S) rDNA gene loci in the tomato genome using a combination of karyotyping and FISH of pachytne chromosomes. Chromosoma 104: 545–550

    Article  Google Scholar 

  40. Zhong X, de Jong JH, and Zabel P (1996) Localization of repetitive sequences on metaphase and pachytene chromosomes of tomato using fluorescence in situ hybridization. Chromosome research 4: 24–28

    Article  Google Scholar 

  41. Zhong X, Fransz PF, Wennekes-van Eden J, Zabel P, Van Kammen A and De Jong JH (1996) High resolution mapping on pachytene chromosomes and extended DNA fibres by fluorescence in situ hybridisation. Plant Molec. Biol. Rep. 14: 232–242

    Article  Google Scholar 

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Fransz, P., de Jong, H., Zabel, P. (1998). Preparation of extended DNA fibres for high resolution mapping by fluorescence in situ hybridization (FISH). In: Gelvin, S.B., Schilperoort, R.A. (eds) Plant Molecular Biology Manual. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-5242-6_4

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  • DOI: https://doi.org/10.1007/978-94-011-5242-6_4

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-011-7657-6

  • Online ISBN: 978-94-011-5242-6

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