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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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2
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Hu Q, Maurais EG, Ly P. Cellular and genomic approaches for exploring structural chromosomal rearrangements. Chromosome Res 2020; 28:19-30. [PMID: 31933061 PMCID: PMC7131874 DOI: 10.1007/s10577-020-09626-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/20/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022]
Abstract
Human chromosomes are arranged in a linear and conserved sequence order that undergoes further spatial folding within the three-dimensional space of the nucleus. Although structural variations in this organization are an important source of natural genetic diversity, cytogenetic aberrations can also underlie a number of human diseases and disorders. Approaches for studying chromosome structure began half a century ago with karyotyping of Giemsa-banded chromosomes and has now evolved to encompass high-resolution fluorescence microscopy, reporter-based assays, and next-generation DNA sequencing technologies. Here, we provide a general overview of experimental methods at different resolution and sensitivity scales and discuss how they can be complemented to provide synergistic insight into the study of human chromosome structural rearrangements. These approaches range from kilobase-level resolution DNA fluorescence in situ hybridization (FISH)-based imaging approaches of individual cells to genome-wide sequencing strategies that can capture nucleotide-level information from diverse sample types. Technological advances coupled to the combinatorial use of multiple methods have resulted in the discovery of new rearrangement classes along with mechanistic insights into the processes that drive structural alterations in the human genome.
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Affiliation(s)
- Qing Hu
- Department of Pathology, Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth G Maurais
- Department of Pathology, Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter Ly
- Department of Pathology, Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Lavania UC, Yamamoto M, Mukai Y. Extended Chromatin and DNA Fibers from Active Plant Nuclei for High-resolution FISH. J Histochem Cytochem 2016; 51:1249-53. [PMID: 14500692 DOI: 10.1177/002215540305101001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The conventional protocol for isolation of cell wall free nuclei for release of DNA fibers for plants involves mechanical removal of the cell wall and separation of debris by sieve filtration. The mechanical grinding pressure applied during the process leaves only the more tolerant G(1) nuclei intact, and all other states of active nuclei that may be present in the target tissues (e.g., leaf) are simply crushed/disrupted during the isolation process. Here we describe an alternative enzymatic protocol for isolation of nuclei from root tip tissue. Cell wall free nuclei at a given stage of cell cycle, free of any cell debris, could be realized in suspension that are fit for preparation of extended fibers suitable for fiber FISH applications. The protocol utilizes selective harvest of active nuclei from root tip tissue in liquid suspension under the influence of cell wall-degrading enzymes, and provides opportunities to target cell cycle-specific nuclei from interphase through division phase for the release of extended DNA fibers. Availability of cell cycle-specific fibers may have added value in transcriptional analysis, DNA:RNA hybridization, visualization of DNA replication and replication forks, and improved FISH efficiency.
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Affiliation(s)
- U C Lavania
- Cytogenetics Division, Central Institute of Medicinal and Aromatic Plants, Lucknow, India.
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4
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New aspects on the structure of neutrophil extracellular traps from chronic obstructive pulmonary disease and in vitro generation. PLoS One 2014; 9:e97784. [PMID: 24831032 PMCID: PMC4022649 DOI: 10.1371/journal.pone.0097784] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/23/2014] [Indexed: 12/21/2022] Open
Abstract
Polymorphonuclear neutrophils have in recent years attracted new attention due to their ability to release neutrophil extracellular traps (NETs). These web-like extracellular structures deriving from nuclear chromatin have been depicted in ambiguous roles between antimicrobial defence and host tissue damage. NETs consist of DNA strands of varying thickness and are decorated with microbicidal and cytotoxic proteins. Their principal structure has in recent years been characterised at molecular and ultrastructural levels but many features that are of direct relevance to cytotoxicity are still incompletely understood. These include the extent of chromatin decondensation during NET formation and the relative amounts and spatial distribution of the microbicidal components within the NET. In the present work, we analyse the structure of NETs found in induced sputum of patients with acutely exacerbated chronic obstructive pulmonary disease (COPD) using confocal laser microscopy and electron microscopy. In vitro induced NETs from human neutrophils serve for purposes of comparison and extended analysis of NET structure. Results demonstrate that COPD sputa are characterised by the pronounced presence of NETs and NETotic neutrophils. We provide new evidence that chromatin decondensation during NETosis is most extensive and generates substantial amounts of double-helix DNA in ‘beads-on-a-string’ conformation. New information is also presented on the abundance and location of neutrophil elastase (NE) and citrullinated histone H3 (citH3). NE occurs in high densities in nearly all non-fibrous constituents of the NETs while citH3 is much less abundant. We conclude from the results that (i) NETosis is an integral part of COPD pathology; this is relevant to all future research on the etiology and therapy of the disease; and that (ii) release of ‘beads-on-a-string’ DNA studded with non-citrullinated histones is a common feature of in vivo NETosis; this is of relevance to both the antimicrobial and the cytotoxic effects of NETs.
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[Chromosomal and genomic aberrations in esophageal squamous cell carcinoma]. YI CHUAN = HEREDITAS 2012; 34:519-25. [PMID: 22659423 DOI: 10.3724/sp.j.1005.2012.00519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies with poor prognosis in China. Patients with ESCC may present with vague symptoms in early stage and most of the cases are diagnosed at advanced stage, without the chance of optimal therapy. In the development and progression of ESCC, cytogenetic and molecular aberrations are frequently observed. This review is to summarize the advances in the chromosomal and genomic alterations of ESCC reported recently.
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O'Brien B, Jossart GH, Ito Y, Greulich-Bode KM, Weier JF, Munne S, Clark OH, Weier HUG. 'Chromosomal Rainbows' Detect Oncogenic Rearrangements of Signaling Molecules in Thyroid Tumors. THE OPEN CELL SIGNALING JOURNAL 2010; 2:13-22. [PMID: 22328910 DOI: 10.2172/1011038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Altered signal transduction can be considered a hallmark of many solid tumors. In thyroid cancers the receptor tyrosine kinase (rtk) genes NTRK1 (Online Mendelian Inheritance in Man = OMIM *191315, also known as 'TRKA'), RET ('Rearranged during Transfection protooncogene', OMIM *164761) and MET (OMIM *164860) have been reported as activated, rearranged or overexpressed. In many cases, a combination of cytogenetic and molecular techniques allows elucidation of cellular changes that initiate tumor development and progression. While the mechanisms leading to overexpression of the rtk MET gene remain largely unknown, a variety of chromosomal rearrangements of the RET or NTKR1 gene could be demonstrated in thyroid cancer. Abnormal expressions in these tumors seem to follow a similar pattern: the rearrangement translocates the 3'- end of the rtk gene including the entire catalytic domain to an expressed gene leading to a chimeric RNA and protein with kinase activity. Our research was prompted by an increasing number of reports describing translocations involving ret and previously unknown translocation partners.We developed a high resolution technique based on fluorescence in situ hybridization (FISH) to allow rapid screening for cytogenetic rearrangements which complements conventional chromosome banding analysis. Our technique applies simultaneous hybridization of numerous probes labeled with different reporter molecules which are distributed along the target chromosome allowing the detection of cytogenetic changes at near megabasepair (Mbp) resolution. Here, we report our results using a probe set specific for human chromosome 10, which is altered in a significant portion of human thyroid cancers (TC's). While rendering accurate information about the cytogenetic location of rearranged elements, our multi-locus, multi-color analysis was developed primarily to overcome limitations of whole chromosome painting (WCP) and chromosome banding techniques for fine mapping of breakpoints in papillary thyroid cancer (PTC).
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Affiliation(s)
- Benjamin O'Brien
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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8
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Mello MLS, Moraes AS, Vidal BC. Extended chromatin fibers and chromatin organization. Biotech Histochem 2010; 86:213-25. [DOI: 10.3109/10520290903549022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Vorsanova SG, Yurov YB, Iourov IY. Human interphase chromosomes: a review of available molecular cytogenetic technologies. Mol Cytogenet 2010; 3:1. [PMID: 20180947 PMCID: PMC2830939 DOI: 10.1186/1755-8166-3-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 01/11/2010] [Indexed: 01/05/2023] Open
Abstract
Human karyotype is usually studied by classical cytogenetic (banding) techniques. To perform it, one has to obtain metaphase chromosomes of mitotic cells. This leads to the impossibility of analyzing all the cell types, to moderate cell scoring, and to the extrapolation of cytogenetic data retrieved from a couple of tens of mitotic cells to the whole organism, suggesting that all the remaining cells possess these genomes. However, this is far from being the case inasmuch as chromosome abnormalities can occur in any cell along ontogeny. Since somatic cells of eukaryotes are more likely to be in interphase, the solution of the problem concerning studying postmitotic cells and larger cell populations is interphase cytogenetics, which has become more or less applicable for specific biomedical tasks due to achievements in molecular cytogenetics (i.e. developments of fluorescence in situ hybridization -- FISH, and multicolor banding -- MCB). Numerous interphase molecular cytogenetic approaches are restricted to studying specific genomic loci (regions) being, however, useful for identification of chromosome abnormalities (aneuploidy, polyploidy, deletions, inversions, duplications, translocations). Moreover, these techniques are the unique possibility to establish biological role and patterns of nuclear genome organization at suprachromosomal level in a given cell. Here, it is to note that this issue is incompletely worked out due to technical limitations. Nonetheless, a number of state-of-the-art molecular cytogenetic techniques (i.e multicolor interphase FISH or interpahase chromosome-specific MCB) allow visualization of interphase chromosomes in their integrity at molecular resolutions. Thus, regardless numerous difficulties encountered during studying human interphase chromosomes, molecular cytogenetics does provide for high-resolution single-cell analysis of genome organization, structure and behavior at all stages of cell cycle.
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Affiliation(s)
- Svetlana G Vorsanova
- Institute of Pediatrics and Children Surgery, Rosmedtechnologii, Moscow, 127412, Russia
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow 119152, Russia
| | - Yuri B Yurov
- Institute of Pediatrics and Children Surgery, Rosmedtechnologii, Moscow, 127412, Russia
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow 119152, Russia
| | - Ivan Y Iourov
- Institute of Pediatrics and Children Surgery, Rosmedtechnologii, Moscow, 127412, Russia
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow 119152, Russia
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Piruska A, Gong M, Sweedler JV, Bohn PW. Nanofluidics in chemical analysis. Chem Soc Rev 2010; 39:1060-72. [DOI: 10.1039/b900409m] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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11
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Fluorescence in situ hybridization on DNA halo preparations and extended chromatin fibres. Methods Mol Biol 2010; 659:21-31. [PMID: 20809301 DOI: 10.1007/978-1-60761-789-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although many fluorescence in situ hybridisation (FISH) protocols involve the use of intact, fixed nuclei, the resolution achieved is not always sufficient, especially for physical mapping. In light of this, several techniques are commonly used to create extended chromatin fibres or extruded loops of DNA. As a result, it is possible to visualise and distinguish regions of the genome at a resolution higher than that attained with conventional preparations for FISH. Such methodologies include fibre-FISH and the DNA halo preparation. While fibre-FISH involves the stretching of chromatin fibres across a glass slide, the DNA halo preparation is somewhat more complex; whereby DNA loops instead of chromatin fibres are generated from interphase nuclei. Furthermore, the DNA halo preparation coupled with FISH is a useful tool for examining interactions between the inextractable nuclear matrix and the cell's genome.In this chapter, we describe how to successfully generate extended chromatin fibres and extruded DNA loops. We will also provide detailed methodologies for coupling either procedure with two distinct FISH procedures; 2D-FISH, which allows for the visualisation of specific chromosomal regions, while telomere peptide nucleic acid (PNA) FISH, enables the detection of all telomeres present within human nuclei.
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12
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Jefferson A, Volpi EV. Fluorescence in situ hybridization (FISH) for genomic investigations in rat. Methods Mol Biol 2010; 659:409-26. [PMID: 20809331 DOI: 10.1007/978-1-60761-789-1_32] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This chapter concentrates on the use of fluorescence in situ hybridization (FISH) for genomic investigations in the laboratory rat (Rattus norvegicus). The selection of protocols included in the chapter has been inspired by a comprehensive range of previously published molecular cytogenetic studies on this model organism, reporting examples of how FISH can be applied for diverse investigative purposes, varying from comparative gene mapping to studies of chromosome structure and genome evolution, to characterization of chromosomes aberrations as well as transgenic insertions. The protocols, which include techniques for the preparation of mitotic chromosomes and DNA fibers from short-term cell cultures, have been gathered through the years and repeatedly tested in our laboratory, and all together aim at providing sufficient experimental versatility to cover a broad range of cytogenetic and cytogenomic applications.
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Affiliation(s)
- Andrew Jefferson
- Department of Cardiovascular Medicine, John Radcliffe Hospital, Oxford, UK
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Weier HUG, Greulich-Bode KM, Wu J, Duell T. Delineating Rearrangements in Single Yeast Artificial Chromosomes by Quantitative DNA Fiber Mapping. ACTA ACUST UNITED AC 2009; 2:15-23. [PMID: 20502619 DOI: 10.2174/1875693x00902010015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human genome; however, appear to have a higher propensity than others to rearrange in any host system. Thus, techniques to detect and accurately characterize such rearrangements need to be developed. We developed a technique termed 'Quantitative DNA Fiber Mapping (QDFM)' that allows accurate tagging of sequence elements of interest with near kilobase accuracy and optimized it for delineation of rearrangements in recombinant DNA clones. This paper demonstrates the power of this microscopic approach by investigating YAC rearrangements. In our examples, high-resolution physical maps for regions within the immunoglobulin lambda variant gene cluster were constructed for three different YAC clones carrying deletions of 95 kb and more. Rearrangements within YACs could be demonstrated unambiguously by pairwise mapping of cosmids along YAC DNA molecules. When coverage by YAC clones was not available, distances between cosmid clones were estimated by hybridization of cosmids onto DNA fibers prepared from human genomic DNA. In addition, the QDFM technology provides essential information about clone stability facilitating closure of the maps of the human genome as well as those of model organisms.
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Affiliation(s)
- Heinz-Ulrich G Weier
- Life Sciences Division, University of California, E.O. Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA
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Herrick J, Bensimon A. Introduction to molecular combing: genomics, DNA replication, and cancer. Methods Mol Biol 2009; 521:71-101. [PMID: 19563102 DOI: 10.1007/978-1-60327-815-7_5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The sequencing of the human genome inaugurated a new era in both fundamental and applied genetics. At the same time, the emergence of new technologies for probing the genome has transformed the field of pharmaco-genetics and made personalized genomic profiling and high-throughput screening of new therapeutic agents all but a matter of routine. One of these technologies, molecular combing, has served to bridge the technical gap between the examination of gross chromosomal abnormalities and sequence-specific alterations. Molecular combing provides a new perspective on the structure and dynamics of the human genome at the whole genome and sub-chromosomal levels with a resolution ranging from a few kilobases up to a megabase and more. Originally developed to study genetic rearrangements and to map genes for positional cloning, recent advances have extended the spectrum of its applications to studying the real-time dynamics of the replication of the genome. Understanding how the genome is replicated is essential for elucidating the mechanisms that both maintain genome integrity and result in the instabilities leading to human genetic disease and cancer. In the following, we will examine recent discoveries and advances due to the application of molecular combing to new areas of research in the fields of molecular cytogenetics and cancer genomics.
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Greulich-Bode KM, Wang M, Rhein AP, Weier JF, Weier HUG. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA. Mol Cytogenet 2008; 1:28. [PMID: 19108707 PMCID: PMC2630919 DOI: 10.1186/1755-8166-1-28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 12/23/2008] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100 kb, careful probe selection and characterization are of paramount importance. RESULTS We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific ~6 kb plasmid onto an unusually small, ~55 kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-kappaB2 locus. CONCLUSION The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.
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Affiliation(s)
- Karin M Greulich-Bode
- Division Genetics of Skin Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, USA
| | - Mei Wang
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, USA
| | - Andreas P Rhein
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, USA
- Klinikum Kaufbeuren, Dr.-Gutermann-Straße 2, D-87600 Kaufbeuren, Germany
| | - Jingly F Weier
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, USA
- Reprogenetics, LLC, Oyster Point Blvd., South San Francisco, CA, USA
| | - Heinz-Ulli G Weier
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, USA
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Santos AP, Wegel E, Allen GC, Thompson WF, Stoger E, Shaw P, Abranches R. In situ methods to localize transgenes and transcripts in interphase nuclei: a tool for transgenic plant research. PLANT METHODS 2006; 2:18. [PMID: 17081287 PMCID: PMC1635696 DOI: 10.1186/1746-4811-2-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2006] [Accepted: 11/02/2006] [Indexed: 05/08/2023]
Abstract
Genetic engineering of commercially important crops has become routine in many laboratories. However, the inability to predict where a transgene will integrate and to efficiently select plants with stable levels of transgenic expression remains a limitation of this technology. Fluorescence in situ hybridization (FISH) is a powerful technique that can be used to visualize transgene integration sites and provide a better understanding of transgene behavior. Studies using FISH to characterize transgene integration have focused primarily on metaphase chromosomes, because the number and position of integration sites on the chromosomes are more easily determined at this stage. However gene (and transgene) expression occurs mainly during interphase. In order to accurately predict the activity of a transgene, it is critical to understand its location and dynamics in the three-dimensional interphase nucleus. We and others have developed in situ methods to visualize transgenes (including single copy genes) and their transcripts during interphase from different tissues and plant species. These techniques reduce the time necessary for characterization of transgene integration by eliminating the need for time-consuming segregation analysis, and extend characterization to the interphase nucleus, thus increasing the likelihood of accurate prediction of transgene activity. Furthermore, this approach is useful for studying nuclear organization and the dynamics of genes and chromatin.
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Affiliation(s)
- Ana Paula Santos
- Plant Genetic Engineering Laboratory, Instituto de Tecnologia Química e Biológica, UNL, Av. República, 2781-901 Oeiras, Portugal
| | - Eva Wegel
- Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH, UK
| | - George C Allen
- Plant Transformation Laboratory (PTL), Departments of Crop Science and Horticultural Science, Campus Box 7550, North Carolina State University, Raleigh, NC 27695, USA
| | - William F Thompson
- Plant Gene Expression Laboratory, Campus Box 7550, North Carolina State University Raleigh, NC 27695, USA
| | - Eva Stoger
- Institute for Molecular Biotechnology, RWTH Aachen, 52074 Aachen, Germany
| | - Peter Shaw
- Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH, UK
| | - Rita Abranches
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica, UNL, Av. República, 2781-901 Oeiras, Portugal
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17
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Lobo NF, Behura SK, Aggarwal R, Chen MS, Collins FH, Stuart JJ. Genomic analysis of a 1 Mb region near the telomere of Hessian fly chromosome X2 and avirulence gene vH13. BMC Genomics 2006; 7:7. [PMID: 16412254 PMCID: PMC1352350 DOI: 10.1186/1471-2164-7-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2005] [Accepted: 01/16/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To have an insight into the Mayetiola destructor (Hessian fly) genome, we performed an in silico comparative genomic analysis utilizing genetic mapping, genomic sequence and EST sequence data along with data available from public databases. RESULTS Chromosome walking and FISH were utilized to identify a contig of 50 BAC clones near the telomere of the short arm of Hessian fly chromosome X2 and near the avirulence gene vH13. These clones enabled us to correlate physical and genetic distance in this region of the Hessian fly genome. Sequence data from these BAC ends encompassing a 760 kb region, and a fully sequenced and assembled 42.6 kb BAC clone, was utilized to perform a comparative genomic study. In silico gene prediction combined with BLAST analyses was used to determine putative orthology to the sequenced dipteran genomes of the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae, and to infer evolutionary relationships. CONCLUSION This initial effort enables us to advance our understanding of the structure, composition and evolution of the genome of this important agricultural pest and is an invaluable tool for a whole genome sequencing effort.
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Affiliation(s)
- Neil F Lobo
- Indiana Center for Insect Genomics, University of Notre Dame, Notre Dame, Indiana, 46556, USA, and Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biological Sciences, Galvin Life Sciences Building, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Susanta K Behura
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Entomology, 505 S Goodwin Ave., University of Illinois, Urbana-Champaign, Il 61801, USA
| | - Rajat Aggarwal
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Ming-Shun Chen
- Department of Entomology, 505 S Goodwin Ave., University of Illinois, Urbana-Champaign, Il 61801, USA
| | - Frank H Collins
- Indiana Center for Insect Genomics, University of Notre Dame, Notre Dame, Indiana, 46556, USA, and Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biological Sciences, Galvin Life Sciences Building, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jeff J Stuart
- Indiana Center for Insect Genomics, University of Notre Dame, Notre Dame, Indiana, 46556, USA, and Purdue University, West Lafayette, Indiana 47907, USA
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
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Yoshido A, Bando H, Yasukochi Y, Sahara K. The Bombyx mori karyotype and the assignment of linkage groups. Genetics 2005; 170:675-85. [PMID: 15802516 PMCID: PMC1450397 DOI: 10.1534/genetics.104.040352] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lepidopteran species have a relatively high number of small holocentric chromosomes (Bombyx mori, 2n = 56). Chromosome identification has long been hampered in this group by the high number and by the absence of suitable markers like centromere position and chromosome bands. In this study, we carried out fluorescence in situ hybridization (FISH) on meiotic chromosome complements using genetically mapped B. mori bacterial artificial chromosomes (BACs) as probes. The combination of two to four either green or red fluorescence-labeled probes per chromosome allowed us to recognize unequivocally each of the 28 bivalents of the B. mori karyotype by its labeling pattern. Each chromosome was assigned one of the already established genetic linkage groups and the correct orientation in the chromosome was defined. This facilitates physical mapping of any other sequence and bears relevance for the ongoing B. mori genome projects. Two-color BAC-FISH karyotyping overcomes the problem of chromosome recognition in organisms where conventional banding techniques are not available.
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Affiliation(s)
- Atsuo Yoshido
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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Ferris MM, Yoshida TM, Marrone BL, Keller RA. Fingerprinting of single viral genomes. Anal Biochem 2005; 337:278-88. [PMID: 15691508 DOI: 10.1016/j.ab.2004.10.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Indexed: 11/30/2022]
Abstract
We demonstrate the use of technology developed for optical mapping to acquire DNA fingerprints from single genomes for the purpose of discrimination and identification of bacteria and viruses. Single genome fingerprinting (SGF) provides not only the size but also the order of the restriction fragments, which adds another dimension to the information that can be used for discrimination. Analysis of single organisms may eliminate the need to culture cells and thereby significantly reduce analysis time. In addition, samples containing mixtures of several organisms can be analyzed. For analysis, cells are embedded in an agarose matrix, lysed, and processed to yield intact DNA. The DNA is then deposited on a derivatized glass substrate. The elongated genome is digested with a restriction enzyme and stained with the intercalating dye YOYO-1. DNA is then quantitatively imaged with a fluorescence microscope and the fragments are sized to an accuracy >or=90% by their fluorescence intensity and contour length. Single genome fingerprints were obtained from pure samples of adenovirus, from bacteriophages lambda and T4 GT7, and from a mixture of the three viral genomes. SGF will enable the fingerprinting of uncultured and unamplified samples and allow rapid identification of microorganisms with applications in forensics, medicine, public health, and environmental microbiology.
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Affiliation(s)
- Matthew M Ferris
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Takeda Y, Mafuné F, Kondow T. Self-organization of histone-jointed three-dimensional DNA network. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2004. [DOI: 10.1016/j.msec.2004.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sahara K, Yoshido A, Kawamura N, Ohnuma A, Abe H, Mita K, Oshiki T, Shimada T, Asano SI, Bando H, Yasukochi Y. W-derived BAC probes as a new tool for identification of the W chromosome and its aberrations in Bombyx mori. Chromosoma 2003; 112:48-55. [PMID: 12827381 DOI: 10.1007/s00412-003-0245-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2003] [Revised: 05/22/2003] [Accepted: 05/28/2003] [Indexed: 10/26/2022]
Abstract
We isolated four W chromosome-derived bacterial artificial chromosome (W-BAC) clones from Bombyx mori BAC libraries by the polymerase chain reaction and used them as probes for fluorescence in situ hybridization (FISH) on chromosome preparations from B. mori females. All four W-BAC probes surprisingly highlighted the whole wild-type W sex chromosome and also identified the entire original W-chromosomal region in W chromosome-autosome translocation mutants. This is the first successful identification of a single chromosome by means of BAC-FISH in species with holokinetic chromosomes. Genomic in situ hybridization (GISH) by using female-derived genomic probes highlighted the W chromosome in a similar chromosome-painting manner. Besides the W, hybridization signals of W-BAC probes also occurred in telomeric and/or subtelomeric regions of the autosomes. These signals coincided well with those of female genomic probes except one additional GISH signal that was observed in a large heterochromatin block of one autosome pair. Our results support the opinion that the B. mori W chromosome accumulated transposable elements and other repetitive sequences that also occur, but scattered, elsewhere in the respective genome.
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Affiliation(s)
- Ken Sahara
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University N9, W9, Kita-ku, Sapporo 060-8589, Japan.
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Cheng Z, Buell CR, Wing RA, Jiang J. Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res 2003; 10:379-87. [PMID: 12296520 DOI: 10.1023/a:1016849618707] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Fluorescence in-situ hybridization (FISH) is a quick and affordable approach to map DNA sequences to specific chromosomal regions. Although FISH is one of the most important physical mapping techniques, research on the resolution of FISH on different cytological targets is scarce in plants. In this study, we report the resolution of FISH mapping on mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers in rice. A majority of the FISH signals derived from bacterial artificial chromosome (BAC) clones separated by approximately 1 Mb of DNA cannot be resolved on mitotic prometaphase chromosomes. In contrast, the relative positions of closely linked or even partially overlapping BAC clones can be resolved on a euchromatic region of rice chromosome 10 at the early pachytene stage. The resolution of pachytene FISH is dependent on early or late pachytene stages and also on the location of the DNA probes in the euchromatic or heterochromatic regions. We calibrated the fiber-FISH technique in rice using seven sequenced BAC clones. The average DNA extension was 3.21 kb/microm among the seven BAC clones. Fiber-FISH results derived from a BAC contig that spanned 1 Mb DNA matched remarkably to the sequencing data, demonstrating the high resolution of this technique in cytological mapping.
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Affiliation(s)
- Zhukuan Cheng
- Department of Horticulture, University of Wisconsin-Madison, 53706, USA
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