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Nuclear genomes of many important plant species are tremendously complicated to map and sequence. The ability to isolate single chromosomes, which represent small units of nuclear genome, is priceless in many areas of plant research including cytogenetics, genomics, and proteomics. Flow cytometry is the only technique which can provide large quantities of pure chromosome fractions suitable for downstream applications including physical mapping, preparation of chromosome-specific BAC libraries, sequencing, and optical mapping. Here, we describe step-by-step procedure of preparation of liquid suspensions of intact mitotic metaphase chromosomes and their flow cytometric analysis and sorting.
Analysis and sorting of plant chromosomes (plant flow cytogenetics) is a special application of flow cytometry in plant genomics and its success depends critically on sample quality. This unit describes the methodology in a stepwise manner, starting with the induction of cell cycle synchrony and accumulation of dividing cells in mitotic metaphase, and continues with the preparation of suspensions of intact mitotic chromosomes, flow analysis and sorting of chromosomes, and finally processing of the sorted chromosomes. Each step of the protocol is described in detail as some procedures have not been used widely. Supporting histograms are presented as well as hints on dealing with plant material; the utility of sorted chromosomes for plant genomics is also discussed. © 2016 by John Wiley & Sons, Inc.
- MeSH
- chromozomy rostlin metabolismus MeSH
- DNA rostlinná genetika MeSH
- hybridizace in situ fluorescenční MeSH
- karyotypizace MeSH
- meristém cytologie účinky léků MeSH
- metafáze účinky léků MeSH
- molekulová hmotnost MeSH
- oxid dusný farmakologie MeSH
- proteomika MeSH
- průtoková cytometrie metody MeSH
- rostliny genetika MeSH
- semena rostlinná účinky léků MeSH
- Publikační typ
- časopisecké články MeSH
Chromosome analysis and sorting using flow cytometry (flow cytogenetics) is an attractive tool for fractionating plant genomes to small parts. The reduction of complexity greatly simplifies genetics and genomics in plant species with large genomes. However, as flow cytometry requires liquid suspensions of particles, the lack of suitable protocols for preparation of solutions of intact chromosomes delayed the application of flow cytogenetics in plants. This chapter outlines a high-yielding procedure for preparation of solutions of intact mitotic chromosomes from root tips of young seedlings and for their analysis using flow cytometry and sorting. Root tips accumulated at metaphase are mildly fixed with formaldehyde, and solutions of intact chromosomes are prepared by mechanical homogenization. The advantages of the present approach include the use of seedlings, which are easy to handle, and the karyological stability of root meristems, which can be induced to high degree of metaphase synchrony. Chromosomes isolated according to this protocol have well-preserved morphology, withstand shearing forces during sorting, and their DNA is intact and suitable for a range of applications.
- MeSH
- buněčný cyklus MeSH
- chromozomy rostlin MeSH
- cytogenetika MeSH
- DNA rostlinná genetika MeSH
- hybridizace in situ fluorescenční metody MeSH
- karyotypizace MeSH
- meristém cytologie MeSH
- průtoková cytometrie metody MeSH
- rostlinné buňky MeSH
- rostliny genetika MeSH
- semena rostlinná růst a vývoj MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Many proteins are present in the nucleus; some are involved with its structural and functional organization, some with gene expression, and some with cell division. The plant nuclear proteome has not been well explored. Its characterization requires extraction methods which minimize both the artifactual alteration of the proteins and the extent of contamination with non-nuclear proteins. The conventional multi-step fractionation procedure is both laborious and prone to contamination. Here, we describe a single-step method based on flow sorting. The method allows the separation of G1, S and G2 phase nuclei and minimizes the risk of contamination by non-nuclear proteins. Preliminary results obtained using G1 phase cell nuclei from barley root tips indicate that flow sorting coupled with a protein/peptide separation and mass spectrometry will permit a comprehensive characterization of the plant nuclear proteome.
Genome analysis in many plant species is hampered by large genome size and by sequence redundancy due to the presence of repetitive DNA and polyploidy. One solution is to reduce the sample complexity by dissecting the genomes to single chromosomes. This can be realized by flow cytometric sorting, which enables purification of chromosomes in large numbers. Coupling the chromosome sorting technology with next generation sequencing provides a targeted and cost effective way to tackle complex genomes. The methods outlined in this article describe a procedure for preparation of chromosomal DNA suitable for next-generation sequencing.
- MeSH
- chromozomy rostlin ultrastruktura MeSH
- délka genomu MeSH
- fluorescenční mikroskopie MeSH
- genom rostlinný * MeSH
- hybridizace in situ fluorescenční MeSH
- ječmen (rod) cytologie genetika MeSH
- klíčení genetika MeSH
- metafáze genetika MeSH
- polyploidie MeSH
- průtoková cytometrie metody MeSH
- pšenice cytologie genetika MeSH
- sekvenční analýza DNA MeSH
- semena rostlinná genetika MeSH
- umělé bakteriální chromozomy MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- žito cytologie genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Practical approach series
3rd ed. xx., 276 s. : il.
- Klíčová slova
- Cytometrie průtoková,
- MeSH
- průtoková cytometrie MeSH
Practical approach series ; 142
3rd ed. [265] s. : il.
- MeSH
- průtoková cytometrie MeSH
- Konspekt
- Buněčná biologie. Cytologie
- NLK Obory
- cytologie, klinická cytologie
279 s.
- Klíčová slova
- Cytometrie průtoková,
- MeSH
- průtoková cytometrie MeSH
- Publikační typ
- příručky MeSH
- Konspekt
- Patologie. Klinická medicína
- NLK Obory
- chemie, klinická chemie
- cytologie, klinická cytologie
Flow cytometric analysis and sorting of plant mitotic chromosomes has been mastered by only a few laboratories worldwide. Yet, it has been contributing significantly to progress in plant genetics, including the production of genome assemblies and the cloning of important genes. The dissection of complex genomes by flow sorting into the individual chromosomes that represent small parts of the genome reduces DNA sample complexity and streamlines projects relying on molecular and genomic techniques. Whereas flow cytometric analysis, that is, chromosome classification according to fluorescence and light scatter properties, is an integral part of any chromosome sorting project, it has rarely been used on its own due to lower resolution and sensitivity as compared to other cytogenetic methods. To perform chromosome analysis and sorting, commercially available electrostatic droplet sorters are suitable. However, in order to resolve and purify chromosomes of interest the instrument must offer high resolution of optical signals as well as stability during long runs. The challenge is thus not the instrumentation, but the adequate sample preparation. The sample must be a suspension of intact mitotic metaphase chromosomes and the protocol, which includes the induction of cell cycle synchrony, accumulation of dividing cells at metaphase, and release of undamaged chromosomes, is time consuming and laborious and needs to be performed very carefully. Moreover, in addition to fluorescent staining chromosomal DNA, the protocol may include specific labelling of DNA repeats to facilitate discrimination of particular chromosomes. This review introduces the applications of chromosome sorting in plants, and discusses in detail sample preparation, chromosome analysis and sorting to achieve the highest purity in flow-sorted fractions, and their suitability for downstream applications.
