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Fransz P, van de Belt J, de Jong H. Extended DNA Fibers for High-Resolution Mapping. Methods Mol Biol 2023; 2672:351-363. [PMID: 37335488 DOI: 10.1007/978-1-0716-3226-0_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
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 mapping.
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Affiliation(s)
- Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
- Wageningen University & Research, Laboratory of Genetics, Wageningen, The Netherlands.
| | - José van de Belt
- Wageningen University & Research, Laboratory of Genetics, Wageningen, The Netherlands
| | - Hans de Jong
- Wageningen University & Research, Laboratory of Genetics, Wageningen, The Netherlands
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Karafiátová M, Bartoš J, Doležel J. Localization of Low-Copy DNA Sequences on Mitotic Chromosomes by FISH. Methods Mol Biol 2017; 1429:49-64. [PMID: 27511166 DOI: 10.1007/978-1-4939-3622-9_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a widely used method to localize DNA sequences on mitotic and meiotic chromosomes and interphase nuclei. It was developed in early 1980s and since then it has contributed to numerous studies and important discoveries. Over the decades, the protocol was modified for ease of use, allowing for localizing multiple probes simultaneously and increasing its sensitivity and specificity. Despite the continuous improvements, the ability to detect short single-copy sequences of only a few kilobases or less, such as genes, remains limited. Here, we provide a detailed protocol for detection of short, single- or low-copy sequences on plant mitotic metaphase chromosomes.
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Affiliation(s)
- Miroslava Karafiátová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78374, Olomouc, Czech Republic.
| | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78374, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78374, Olomouc, Czech Republic
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Yang K, Zhang Y, Converse R, Lv J, Shi M, Zhang H, Zhu L. Improvement of high-resolution fluorescence in situ hybridisation mapping on chromosomes of Brassica oleracea var. capitata. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:325-331. [PMID: 26312399 DOI: 10.1111/plb.12384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 08/22/2015] [Indexed: 06/04/2023]
Abstract
The low resolution of chromosome-based Fluorescence in situ hybridisation (FISH) mapping is primarily due to the structure of the plant cell wall and cytoplasm and the compactness of regular chromosomes, which represent a significant obstacle to FISH. In order to improve spatial resolution and signal detection sensitivity, we provide a reproducible method to generate high-quality extended chromosomes that are ~13 times as long as their pachytene counterparts. We demonstrate that proteinase K used in this procedure is crucial for stretching pachytene chromosomes of Brassica oleracea in the context of a modified Carnoy's II fixative (6:1:3, ethanol:chloroform:acetic acid). The quality of super-stretched chromosomes was assessed in several FISH experiments. FISH signals from both repetitive 5S rDNA and single-copy ARC1 on super-stretched chromosomes are brighter than those on other different types of chromosome due to enhanced accessibility to targets on stretched pachytene chromosomes. In conclusion, the resulting extended chromosomes are suitable for FISH mapping for repetitive DNA sequences and the localisation of a single-copy locus, and FISH performed on super-stretched chromosomes can achieve significantly higher sensitivity and spatial resolution than other chromosome-based FISH mapping techniques.
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Affiliation(s)
- K Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Y Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - R Converse
- Cincinnati State Technical and Community College, Cincinnati, OH, USA
| | - J Lv
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - M Shi
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - H Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - L Zhu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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Abstract
Analysis of the formation of extended chromatin fibers (ECFs) in response to the action of gravity following lysis by hypertonic and detergent solutions is a useful technical procedure relevant for studies of the positioning of particular DNA signals on chromatin filaments. Additionally, if toluidine blue molecules are allowed to bind electrostatically to available DNA phosphates on ECFs, the birefringence brightness generated in these filaments, as observed by polarization microscopy, facilitates the description of the frequency of ECF formation and extension of the chromatin filaments generated. Thus, different patterns of DNA-nuclear matrix protein associations related to varying transcriptional activities and chromatin organization in isolated cells can be assessed. A technique for producing ECFs in different isolated cell types under variable physiological and/or pathological conditions is detailed in this chapter.
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Affiliation(s)
- Maria Luiza S Mello
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
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Abstract
This chapter describes the various methods derived from the protocol of standard fluorescent in situ hybridization (FISH) that are used in human, animal, plant, and microbial studies. These powerful techniques allow us to detect and physically map on interphase nuclei, chromatin fibers, or metaphase chromosomes probes derived from single-copy genes to repetitive DNA sequences. Other variants of the technique enable the co-localization of genes and the overall comparison of the genome among individuals of the same species or of different taxa. A further variant detects and localizes bacteria on tissues and cells. Overall, this offers a remarkable multiplicity of possible applications ranging from strict physical mapping, to clinical and evolutionary studies, making it a powerful and informative complement to other molecular, functional, or genomic approaches.
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Karafiátová M, Bartoš J, Kopecký D, Ma L, Sato K, Houben A, Stein N, Doležel J. Mapping nonrecombining regions in barley using multicolor FISH. Chromosome Res 2013; 21:739-51. [DOI: 10.1007/s10577-013-9380-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 12/22/2022]
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