Abstract
DNA fiber-FISH is an easy and simple light microscopic method to map unique and repeat sequences relative to each other at the molecular scale. A standard fluorescence microscope and a DNA labeling kit are sufficient to visualize DNA sequences from any tissue or organ. Despite the enormous progress of high-throughput sequencing technologies, DNA fiber-FISH remains a unique and indispensable tool to detect chromosomal rearrangements and to demonstrate differences between related species at high resolution. We discuss standard and alternative steps to easily prepare extended DNA fibers for high-resolution FISH map**.
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References
Pardue ML, Gall JG (1969) Molecular hybridization of radioactive DNA to the DNA of cytological preparations. Proc Natl Acad Sci 64:600–604
Volpi EV, Bridger JM (2008) FISH glossary: an overview of the fluorescence in situ hybridization technique. BioTechniques 45:385–409
Jiang J (2019) Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosom Res 27:153–165
Heng HH, Squire J, Tsui LC (1992) High-resolution map** of mammalian genes by in situ hybridization to free chromatin. Proc Natl Acad Sci 89:9509–9513
Wiegant J, Kalle W, Mullenders L, Brookes S, Hoovers JMN, Dauwerse JG, Van Ommen GJB, Raap AK (1992) High-resolution in situ hybridization using DNA halo preparations. Hum Mol Genet 1:587–591
Fransz PF, Alonso-Blanco C, Liharska TB, Peeters AJM, Zabel P, Jong JH (1996) High-resolution physical map** in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J 9(3):421–430
de Jong JH, Fransz P, Zabel P (1999) High resolution FISH in plants – techniques and applications. Trends Plant Sci 4:258–263
Cook PR, Brazell IA, Jost E (1976) Characterization of nuclear structures containing superhelical DNA. J Cell Sci 22:303–324
Vogelstein B, Pardoll DM, Coffey DS (1980) Supercoiled loops and eucaryotic DNA replication. Cell 22:79–85
Cohen SM, Chastain PD, Cordeiro-Stone M, Kaufman DG (2009) DNA replication and the GINS complex: localization on extended chromatin fibers. Epigenetics Chromatin 2:6–6
Blower MD, Sullivan BA, Karpen GH (2002) Conserved organization of centromeric chromatin in flies and humans. Dev Cell 2:319–330
** W, Melo JR, Nagaki K, Talbert PB, Henikoff S, Dawe RK, Jiang J (2004) Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell Online 16:571–581
Fidlerová H, Senger G, Kost M, Sanseau P, Sheer D (1994) Two simple procedures for releasing chromatin from routinely fixed cells for fluorescence in situ hybridization. Cytogenet Genome Res 65:203–205
Gerdes MG, Carter KC, Moen PT, 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
Koo D, Jiang J (2009) Super-stretched pachytene chromosomes for fluorescence in situ hybridization map** and immunodetection of DNA methylation. Plant J 59:509–516
Valárik M, Bartoš J, Kovářová P, Kubaláková M, De Jong JH, Doležel J (2004) High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J 37:940–950
Bensimon A, Simon A, Chiffaudel A, Croquette V, Heslot F, Bensimon D (1994) Alignment and sensitive detection of DNA by a moving interface. Science 265:2096–2098
Weier H-UG, Wang L, Mullikin JC, Zhu Y, Cheng J-F, Greulich KM, Bensimon A, Gray JW (1995) Quantitative DNA fiber map**. Hum Mol Genet 4:1903–1910
Jackson SA, Dong F, Jiang J (1999) Digital map** of bacterial artificial chromosomes by fluorescence in situ hybridization. Plant J 17(5):581–587
Houseal TW, Dackowski WR, Landes GM, Klinger KW (1994) High resolution map** of overlap** cosmids by fluorescence in situ hybridization. Cytometry 15:193–198
Parra I, Windle B (1993) High resolution visual map** of stretched DNA by fluorescent hybridization. Nat Genet 5:17–21
Fransz P, de Jong H, Zabel P (1998) Plant molecular biology manual, pp 49–66. https://doi.org/10.1007/978-94-011-5242-6_4
Dechyeva D, Schmidt T (2016) Plant cytogenetics, methods and protocols. Methods Mol Biol 1429:23–33
Yang K, Zhang H, Converse R, Wang Y, Rong X, Wu Z, Luo B, Xue L, Jian L, Zhu L, Wang X (2011) Fluorescence in situ hybridization on plant extended chromatin DNA fibers for single-copy and repetitive DNA sequences. Plant Cell Rep 30:1779
Zhang W, Lee H-R, Koo D-H, Jiang J (2008) Epigenetic modification of centromeric chromatin: hypomethylation of DNA sequences in the CENH3-associated chromatin in Arabidopsis thaliana and maize. Plant Cell 20:25–34
Weier H-UG (2001) DNA fiber map** techniques for the assembly of high-resolution physical maps. J Histochem Cytochem 49:939–948
Lysak M, Fransz P, Schubert I (2006) Cytogenetic analyses of Arabidopsis. Methods Mol Biol 323:173–186. https://doi.org/10.1385/1-59745-003-0:173
Bey TD, Koini M, Fransz P (2017) Plant chromatin dynamics, methods and protocols. Methods Mol Biol 1675:467–480
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Fransz, P., van de Belt, J., de Jong, H. (2023). Extended DNA Fibers for High-Resolution Map**. In: Heitkam, T., Garcia, S. (eds) Plant Cytogenetics and Cytogenomics. Methods in Molecular Biology, vol 2672. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3226-0_22
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DOI: https://doi.org/10.1007/978-1-0716-3226-0_22
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