1
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Adel S, Carels N. Plant Tolerance to Drought Stress with Emphasis on Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112170. [PMID: 37299149 DOI: 10.3390/plants12112170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 06/12/2023]
Abstract
Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.
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Affiliation(s)
- Sarah Adel
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Nicolas Carels
- Laboratory of Biological System Modeling, Center of Technological Development for Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro 21040-361, Brazil
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2
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Maass PG, Barutcu AR, Rinn JL. Interchromosomal interactions: A genomic love story of kissing chromosomes. J Cell Biol 2018; 218:27-38. [PMID: 30181316 PMCID: PMC6314556 DOI: 10.1083/jcb.201806052] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/27/2018] [Accepted: 08/01/2018] [Indexed: 01/26/2023] Open
Abstract
Maass et al. review interchromosomal interactions, which, like intrachromosomal interactions, are emerging as important regulators of genome organization and gene expression. Nuclei require a precise three- and four-dimensional organization of DNA to establish cell-specific gene-expression programs. Underscoring the importance of DNA topology, alterations to the nuclear architecture can perturb gene expression and result in disease states. More recently, it has become clear that not only intrachromosomal interactions, but also interchromosomal interactions, a less studied feature of chromosomes, are required for proper physiological gene-expression programs. Here, we review recent studies with emerging insights into where and why cross-chromosomal communication is relevant. Specifically, we discuss how long noncoding RNAs (lncRNAs) and three-dimensional gene positioning are involved in genome organization and how low-throughput (live-cell imaging) and high-throughput (Hi-C and SPRITE) techniques contribute to understand the fundamental properties of interchromosomal interactions.
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Affiliation(s)
- Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA .,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA.,University of Colorado, BioFrontiers, Department of Biochemistry, Boulder, CO
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3
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Abstract
The wheat genome encodes some 100,000 genes. To understand how the expression of these genes is regulated it will be necessary to carry out many genetic transformation experiments. Robust protocols that allow scientists to transform a wide range of wheat genotypes are therefore required. In this chapter, we describe a protocol for biolistic transformation of wheat that uses immature embryos and small quantities of DNA cassettes. An original method for DNA cassette purification is also described. This protocol can be used to transform a wide range of wheat genotypes and other related species.
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4
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Santos AP, Ferreira LJ, Oliveira MM. Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses. BIOLOGY 2017; 6:biology6010003. [PMID: 28275209 PMCID: PMC5371996 DOI: 10.3390/biology6010003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/05/2017] [Accepted: 01/10/2017] [Indexed: 12/12/2022]
Abstract
The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs) or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants) are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype. The inheritability of epigenetic marks and chromatin configurations along successive generations are interpreted as a way for plants to “communicate” past experiences of stress sensing. A mechanistic understanding of chromatin and epigenetics plasticity in plant response to stress, including tissue- and genotype-specific epigenetic patterns, may help to reveal the epigenetics contributions for genome and phenotype regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
| | - Liliana J Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
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5
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Rodriguez-Granados NY, Ramirez-Prado JS, Veluchamy A, Latrasse D, Raynaud C, Crespi M, Ariel F, Benhamed M. Put your 3D glasses on: plant chromatin is on show. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3205-21. [PMID: 27129951 DOI: 10.1093/jxb/erw168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The three-dimensional organization of the eukaryotic nucleus and its chromosomal conformation have emerged as important features in the complex network of mechanisms behind gene activity and genome connectivity dynamics, which can be evidenced in the regionalized chromosomal spatial distribution and the clustering of diverse genomic regions with similar expression patterns. The development of chromatin conformation capture (3C) techniques has permitted the elucidation of commonalities between the eukaryotic phyla, as well as important differences among them. The growing number of studies in the field performed in plants has shed light on the structural and regulatory features of these organisms. For instance, it has been proposed that plant chromatin can be arranged into different conformations such as Rabl, Rosette-like, and Bouquet, and that both short- and long-range chromatin interactions occur in Arabidopsis. In this review, we compile the current knowledge about chromosome architecture characteristics in plants, as well as the molecular events and elements (including long non-coding RNAs, histone and DNA modifications, chromatin remodeling complexes, and transcription factors) shaping the genome three-dimensional conformation. Furthermore, we discuss the developmental outputs of genome topology-mediated gene expression regulation. It is becoming increasingly clear that new tools and techniques with higher resolution need to be developed and implemented in Arabidopsis and other model plants in order to better understand chromosome architecture dynamics, from an integrative perspective with other fields of plant biology such as development, stress biology, and finally agriculture.
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Affiliation(s)
- Natalia Y Rodriguez-Granados
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Juan S Ramirez-Prado
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Federico Ariel
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Moussa Benhamed
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
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6
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The distribution of cotransformed transgenes in particle bombardment-mediated transformed wheat. Transgenic Res 2015; 24:1055-63. [PMID: 26405007 DOI: 10.1007/s11248-015-9906-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/19/2015] [Indexed: 10/23/2022]
Abstract
Although particle bombardment is the predominant method of foreign DNA direct transfer, whether transgene is integrated randomly into the genome has not been determined. In this study, we identified the distribution of transgene loci in 45 transgenic wheat (Triticum aestivum L.) lines containing co-transformed high molecular weight glutenin subunit genes and the selectable marker bar using fluorescence in situ hybridization. Transgene loci were shown to distribute unevenly throughout the genome and incorporate into different locations along individual chromosomes. There was only a slight tendency towards the localization of transgenes in distal chromosome regions. High proportions of transgenes in separate plasmids integrated at the same site and only 7 lines had 2 or 3 loci. Such loci may not segregate frequently in subsequent generations so it is difficult to remove selectable markers from transgenic lines after regeneration. We also found that three transgene lines were associated with rearranged chromosomes, suggesting a the close relationship between particle bombardment-mediated transgene integration and chromosomal rearrangements.
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7
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Blechl AE, Vensel WH. Variant high-molecular-weight glutenin subunits arising from biolistic transformation of wheat. J Cereal Sci 2013. [DOI: 10.1016/j.jcs.2013.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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8
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Schubert I, Shaw P. Organization and dynamics of plant interphase chromosomes. TRENDS IN PLANT SCIENCE 2011; 16:273-81. [PMID: 21393049 DOI: 10.1016/j.tplants.2011.02.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 02/01/2011] [Accepted: 02/05/2011] [Indexed: 05/23/2023]
Abstract
Eukaryotic chromosomes occupy distinct territories within interphase nuclei. The arrangement of chromosome territories (CTs) is important for replication, transcription, repair and recombination processes. Our knowledge about interphase chromatin arrangement is mainly based on results from in situ labeling approaches. The phylogenetic affiliation of a species, cell cycle, differentiation status and environmental factors are all likely to influence interphase nuclear architecture. In this review we survey current data about relative positioning of CTs, somatic pairing of homologs, and sister chromatid alignment in meristematic and differentiated tissues, using data derived mainly from Arabidopsis thaliana, wheat (Triticum aestivum) and their relatives. We discuss morphological constraints and epigenetic impacts on nuclear architecture, the evolutionary stability of CT arrangements, and alterations of nuclear architecture during transcription and repair.
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Affiliation(s)
- Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D06466 Gatersleben, Germany.
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9
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Santos A, Ferreira L, Maroco J, Oliveira M. Abiotic Stress and Induced DNA Hypomethylation Cause Interphase Chromatin Structural Changes in Rice rDNA Loci. Cytogenet Genome Res 2011; 132:297-303. [DOI: 10.1159/000322287] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2010] [Indexed: 01/30/2023] Open
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10
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Park HM, Jeon EJ, Waminal NE, Shin KS, Kweon SJ, Park BS, Suh SC, Kim HH. Detection of transgenes in three genetically modified rice lines by fluorescence in situ hybridization. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0064-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Ramessar K, Rademacher T, Sack M, Stadlmann J, Platis D, Stiegler G, Labrou N, Altmann F, Ma J, Stöger E, Capell T, Christou P. Cost-effective production of a vaginal protein microbicide to prevent HIV transmission. Proc Natl Acad Sci U S A 2008; 105:3727-32. [PMID: 18316741 PMCID: PMC2268773 DOI: 10.1073/pnas.0708841104] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Indexed: 11/18/2022] Open
Abstract
A series of small-molecule microbicides has been developed for vaginal delivery to prevent heterosexual HIV transmission, but results from human clinical trials have been disappointing. Protein-based microbicides, such as HIV-specific monoclonal antibodies, have been considered as an alternative approach. Despite their promising safety profile and efficacy, the major drawback of such molecules is the economy of large-scale production in mammalian cells, the current system of choice. Here, we show that an alternative biomanufacturing platform is now available for one of the most promising anti-HIV antibodies (2G12). Our data show that the HIV-neutralization capability of the antibody is equal to or superior to that of the same antibody produced in CHO cells. We conclude that this protein production system may provide a means to achieve microbicide ingredient manufacture at costs that would allow product introduction and manufacture in the developing world.
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Affiliation(s)
- Koreen Ramessar
- *Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Avenida Alcalde Rovira Roure, 191, Lleida, 25198, Spain
| | - Thomas Rademacher
- Institute for Molecular Biotechnology, Biology VII, RWTH Aachen, Worringerweg 1, 52074 Aachen, Germany
| | - Markus Sack
- Institute for Molecular Biotechnology, Biology VII, RWTH Aachen, Worringerweg 1, 52074 Aachen, Germany
| | - Johannes Stadlmann
- Department of Chemistry, Glycobiology Division, University of Natural Resources and Applied Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Dimitris Platis
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | | | - Nikos Labrou
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Fritz Altmann
- Department of Chemistry, Glycobiology Division, University of Natural Resources and Applied Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Julian Ma
- Saint George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom; and
| | - Eva Stöger
- Institute for Molecular Biotechnology, Biology VII, RWTH Aachen, Worringerweg 1, 52074 Aachen, Germany
| | - Teresa Capell
- *Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Avenida Alcalde Rovira Roure, 191, Lleida, 25198, Spain
| | - Paul Christou
- *Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Avenida Alcalde Rovira Roure, 191, Lleida, 25198, Spain
- **Institucio Catalana de Recerca i Estudis Avancats, 08010 Barcelona, Spain
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12
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Chromosome kissing. Curr Opin Genet Dev 2007; 17:443-50. [PMID: 17933509 DOI: 10.1016/j.gde.2007.08.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 07/27/2007] [Accepted: 08/31/2007] [Indexed: 11/23/2022]
Abstract
Eukariotic chromosomes occupy distinct territories in the cell nucleus. These territories intermingle little with other chromosomes. Nevertheless, several contacts between different chromosomal loci have been documented, a phenomenon called chromosome kissing. Some of these contacts may arise simply because of preferred chromosome neighborhoods and of the sharing of transcriptional machineries, while others seem to have exquisite regulatory functions. Recent approaches that allow to detect chromosome kissing events in an unbiased manner suggest that chromatin folding is such that cis contacts with neighboring elements are most frequent, but contacts with remote parts of the same chromosome or with different chromosomes are possible. These contacts are modulated by specific chromatin features of each locus, and they may play important roles in the regulation of gene expression. Chromosome kissing events may also be at the origin of chromosomal rearrangements.
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13
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Gómez-Galera S, Pelacho AM, Gené A, Capell T, Christou P. The genetic manipulation of medicinal and aromatic plants. PLANT CELL REPORTS 2007; 26:1689-715. [PMID: 17609957 DOI: 10.1007/s00299-007-0384-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 05/04/2007] [Accepted: 05/11/2007] [Indexed: 05/16/2023]
Abstract
Medicinal and aromatic plants have always been intimately linked with human health and culture. Plant-derived medicines constitute a substantial component of present day human healthcare systems in industrialized as well as developing countries. They are products of plant secondary metabolism and are involved in many other aspects of a plant's interaction with its immediate environment. The genetic manipulation of plants together with the establishment of in vitro plant regeneration systems facilitates efforts to engineer secondary product metabolic pathways. Advances in the cloning of genes involved in relevant pathways, the development of high throughput screening systems for chemical and biological activity, genomics tools and resources, and the recognition of a higher order of regulation of secondary plant metabolism operating at the whole plant level facilitate strategies for the effective manipulation of secondary products in plants. Here, we discuss advances in engineering metabolic pathways for specific classes of compounds in medicinal and aromatic plants and we identify remaining constraints and future prospects in the field. In particular we focus on indole, tropane, nicotine, isoquinoline alcaloids, monoterpenoids such as menthol and related compounds, diterpenoids such as taxol, sequiterpenoids such as artemisinin and aromatic amino acids.
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Affiliation(s)
- Sonia Gómez-Galera
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
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14
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Abstract
At certain evolutionary junctures, two or more mutations participating in the build-up of a new complex function may be required to become available simultaneously in the same individuals. How could this happen in higher organisms whose populations are small compared to those of microbes, and in which chances of combined nearly simultaneous highly specific favorable mutations are correspondingly low? The question can in principle be answered for regulatory evolution, one of the basic processes of evolutionary change. A combined resetting of transcription rates in several genes could occur in the same individual. It is proposed that, in eukaryotes, changes in epigenetic trends and epigenetically transforming encounters between alternative chromatin structures could arise frequently enough so as to render probable particular conjunctions of changed transcription rates. Such conjunctions could involve mutational changes with low specificity requirements in gene-associated regions of non-protein-coding sequences. The effects of such mutations, notably when they determine the use of histone variants and covalent modifications of histones, can be among those that migrate along chromatin. Changes in chromatin structure are often cellularly inheritable over at least a limited number of generations of cells, and of individuals when the germ line is involved. SINEs and LINEs, which have been considered "junk DNA", are among the repeat sequences that would appear liable to have teleregulatory effects on the function of a nearby promoter, through changes in their numbers and distribution. There may also be present preexisting unstably inheritable epigenetic trends leading to cellular variegation, trends endemic in a cell population based on DNA sequences previously established in the neighborhood. Either way, epigenetically conditioned teleregulatory trends may display only limited penetrance. The imposition at a distance of new chromatin structures with regulatory impact can occur in cis as well as in trans, and is examined as intrachromosomally spreading teleregulation and interchromosomal "gene kissing". The chances for two or more particular epigenetically determined regulatory trends to occur together in a cell are increased thanks to the proposed low specificity requirements for most of the pertinent sequence changes in intergenic and intronic DNA or in the distribution of middle repetitive sequences that have teleregulatory impact. Inheritable epigenetic changes ("epimutations") with effects at a distance would then perdure over the number of generations required for "assimilation" of the several regulatory novelties through the occurrence and selection, gene by gene, of specific classical mutations. These mutations would have effects similar to the epigenetic effects, yet would provide stability and penetrance. The described epigenetic/genetic partnership may well at times have opened the way toward certain complex new functions. Thus, the presence of "junk DNA", through co-determining the (higher or lower) order and the variants of chromatin structure with regulatory effects at a distance, might make an important contribution to the evolution of complex organisms.
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Affiliation(s)
- Emile Zuckerkandl
- Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
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15
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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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16
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Schoenenberger N, Guadagnuolo R, Savova-Bianchi D, Küpfer P, Felber F. Molecular analysis, cytogenetics and fertility of introgression lines from transgenic wheat to Aegilops cylindrica host. Genetics 2006; 174:2061-70. [PMID: 17028347 PMCID: PMC1698652 DOI: 10.1534/genetics.106.058529] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Natural hybridization and backcrossing between Aegilops cylindrica and Triticum aestivum can lead to introgression of wheat DNA into the wild species. Hybrids between Ae. cylindrica and wheat lines bearing herbicide resistance (bar), reporter (gus), fungal disease resistance (kp4), and increased insect tolerance (gna) transgenes were produced by pollination of emasculated Ae. cylindrica plants. F1 hybrids were backcrossed to Ae. cylindrica under open-pollination conditions, and first backcrosses were selfed using pollen bags. Female fertility of F1 ranged from 0.03 to 0.6%. Eighteen percent of the sown BC1s germinated and flowered. Chromosome numbers ranged from 30 to 84 and several of the plants bore wheat-specific sequence-characterized amplified regions (SCARs) and the bar gene. Self fertility in two BC1 plants was 0.16 and 5.21%, and the others were completely self-sterile. Among 19 BC1S1 individuals one plant was transgenic, had 43 chromosomes, contained the bar gene, and survived glufosinate treatments. The other BC1S1 plants had between 28 and 31 chromosomes, and several of them carried SCARs specific to wheat A and D genomes. Fertility of these plants was higher under open-pollination conditions than by selfing and did not necessarily correlate with even or euploid chromosome number. Some individuals having supernumerary wheat chromosomes recovered full fertility.
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Affiliation(s)
- Nicola Schoenenberger
- Laboratoire de Botanique Evolutive, Institut de Botanique, Université de Neuchâtel, 2007 Neuchâtel, Switzerland.
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17
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Kohli A, Melendi PG, Abranches R, Capell T, Stoger E, Christou P. The Quest to Understand the Basis and Mechanisms that Control Expression of Introduced Transgenes in Crop Plants. PLANT SIGNALING & BEHAVIOR 2006; 1:185-95. [PMID: 19521484 PMCID: PMC2634025 DOI: 10.4161/psb.1.4.3195] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Accepted: 07/12/2006] [Indexed: 05/19/2023]
Abstract
We discuss mechanisms and factors that influence levels and stability of expressed heterologous proteins in crop plants. We have seen substantial progress in this field over the past two decades in model experimental organisms such as Arabidopsis and tobacco. There is no question such studies have resulted in furthering our understanding of key processes in the plant cell and the elaboration of sophisticated models to explain underlying mechanisms that might influence the fate, levels and stability of expression of recombinant heterologous proteins in plants. However, very often, such information is not applicable outside these laboratory experimental models. In order to generate a knowledge basis that can be used to achieve high levels and stability of heterologous proteins in relevant crop plants it is imperative to perform such studies on the target crops. With this in mind, we discuss key elements of the process at the DNA, RNA and protein levels. We believe it is essential to discuss recombinant protein production in crops in a holistic manner in order to develop a comprehensive knowledge base that will in turn serve plant biotechnology applications well.
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Affiliation(s)
- Ajay Kohli
- Institute for Research on Environment & Sustainability (IRES); University of Newcastle upon Tyne; Newcastle, UK
| | | | - Rita Abranches
- Instituto de Tecnologia Quimica e Biologica; Plant Cell Biology Laboratory; Oeiras, Portugal and Universidade Nova de Lisboa
| | | | - Eva Stoger
- Biology VII; RWTH Aachen; Aachen, Germany
| | - Paul Christou
- ICREA; Department de Produccio Vegetal I Ciencia Forestal; Lleida, Spain
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Grimaud C, Bantignies F, Pal-Bhadra M, Ghana P, Bhadra U, Cavalli G. RNAi Components Are Required for Nuclear Clustering of Polycomb Group Response Elements. Cell 2006; 124:957-71. [PMID: 16530043 DOI: 10.1016/j.cell.2006.01.036] [Citation(s) in RCA: 246] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Revised: 12/02/2005] [Accepted: 01/17/2006] [Indexed: 01/14/2023]
Abstract
Drosophila Polycomb group (PcG) proteins silence homeotic genes through binding to Polycomb group response elements (PREs). Fab-7 is a PRE-containing regulatory element from the homeotic gene Abdominal-B. When present in multiple copies in the genome, Fab-7 can induce long-distance gene contacts that enhance PcG-dependent silencing. We show here that components of the RNA interference (RNAi) machinery are involved in PcG-mediated silencing at Fab-7 and in the production of small RNAs at transgenic Fab-7 copies. In general, these mutations do not affect the recruitment of PcG components, but they are specifically required for the maintenance of long-range contacts between Fab-7 copies. Dicer-2, PIWI, and Argonaute1, three RNAi components, frequently colocalize with PcG bodies, and their mutation significantly reduces the frequency of PcG-dependent chromosomal associations of endogenous homeotic genes. This suggests a novel role for the RNAi machinery in regulating the nuclear organization of PcG chromatin targets.
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Affiliation(s)
- Charlotte Grimaud
- Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
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19
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Schoenenberger N, Felber F, Savova-Bianchi D, Guadagnuolo R. Introgression of wheat DNA markers from A, B and D genomes in early generation progeny of Aegilops cylindrica Host x Triticum aestivum L. hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1338-46. [PMID: 16133306 DOI: 10.1007/s00122-005-0063-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Accepted: 07/25/2005] [Indexed: 05/04/2023]
Abstract
Introgression from allohexaploid wheat (Triticum aestivum L., AABBDD) to allotetraploid jointed goatgrass (Aegilops cylindrica Host, CCDD) can take place in areas where the two species grow in sympatry and hybridize. Wheat and Ae. cylindrica share the D genome, issued from the common diploid ancestor Aegilops tauschii Coss. It has been proposed that the A and B genome of bread wheat are secure places to insert transgenes to avoid their introgression into Ae. cylindrica because during meiosis in pentaploid hybrids, A and B genome chromosomes form univalents and tend to be eliminated whereas recombination takes place only in D genome chromosomes. Wheat random amplified polymorphic DNA (RAPD) fragments, detected in intergeneric hybrids and introgressed to the first backcross generation with Ae. cylindrica as the recurrent parent and having a euploid Ae. cylindrica chromosome number or one supernumerary chromosome, were assigned to wheat chromosomes using Chinese Spring nulli-tetrasomic wheat lines. Introgressed fragments were not limited to the D genome of wheat, but specific fragments of A and B genomes were also present in the BC1. Their presence indicates that DNA from any of the wheat genomes can introgress into Ae. cylindrica. Successfully located RAPD fragments were then converted into highly specific and easy-to-use sequence characterised amplified regions (SCARs) through sequencing and primer design. Subsequently these markers were used to characterise introgression of wheat DNA into a BC1S1 family. Implications for risk assessment of genetically modified wheat are discussed.
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Affiliation(s)
- N Schoenenberger
- Laboratoire de Botanique Evolutive, Institut de Botanique, Université de Neuchâtel, Neuchâtel, Switzerland.
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20
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Wegel E, Shaw PJ. Chromosome organization in wheat endosperm and embryo. Cytogenet Genome Res 2005; 109:175-80. [PMID: 15753574 DOI: 10.1159/000082397] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2003] [Accepted: 02/02/2004] [Indexed: 11/19/2022] Open
Abstract
We have analysed the chromosome organization in endosperm and embryo of bread wheat (Triticum aestivum L.), in order to compare these tissues with developing anthers, in which the centromeres associate, and the developing root xylem vessel cells, in which the chromosomes endoreduplicate to become polytene and associate via their centromeres. Both endosperm and embryo showed a typical Rabl configuration and a degree of non-homologous centromere association and the endosperm also showed extensive telomere association. Wheat endosperm is initially triploid and during its development a percentage of the nuclei increase their DNA content to 6C and 12C. 6C nuclei showed twice as many centromeres as 3C nuclei and the centromere number increased further in 12C nuclei. The higher the C-content of a nucleus the more the telomeres associated in endosperm. The vast majority of 12C nuclei showed six rye chromosome arms, although a few showed three associated groups of rye chromosome arms. This means that during endosperm development wheat nuclei show both polyploidization and polytenization.
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Affiliation(s)
- E Wegel
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
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21
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Pecinka A, Kato N, Meister A, Probst AV, Schubert I, Lam E. Tandem repetitive transgenes and fluorescent chromatin tags alter local interphase chromosome arrangement in Arabidopsis thaliana. J Cell Sci 2005; 118:3751-8. [PMID: 16076901 DOI: 10.1242/jcs.02498] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluorescent protein chromatin tagging as achieved by the lac operator/lac repressor system is useful to trace distinct chromatin domains in living eukaryotic nuclei. To interpret the data correctly, it is important to recognize influences of the tagging system on nuclear architecture of the host cells. Within an Arabidopsis line that carries lac operator/lac repressor/GFP transgenes, the transgene loci frequently associate with each other and with heterochromatic chromocenters. Accumulation of tagged fusion protein further enhances the association frequency. Independent experiments with a transgenic plant carrying another multi-copy transgene also revealed, independent of its transcriptional state, unusually high frequencies of association with each other and with heterochromatin. From these results we conclude that the lac operator/lac repressor chromatin tagging system may alter the spatial chromatin organization in the host nuclei (in particular when more than one insertion locus is present) and also that loci of homologous transgenic repeats associate more often with each other and with endogenous heterochromatin than normal euchromatic regions.
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Affiliation(s)
- Ales Pecinka
- Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
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22
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Stam M, Mittelsten Scheid O. Paramutation: an encounter leaving a lasting impression. TRENDS IN PLANT SCIENCE 2005; 10:283-90. [PMID: 15949762 DOI: 10.1016/j.tplants.2005.04.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 03/07/2005] [Accepted: 04/26/2005] [Indexed: 05/02/2023]
Abstract
Paramutation is the result of heritable changes in gene expression that occur upon interaction between alleles. Whereas Mendelian rules, together with the concept of genetic transmission via the DNA sequence, can account for most inheritance in sexually propagating organisms, paramutation-like phenomena challenge the exclusiveness of Mendelian inheritance. Most paramutation-like phenomena have been observed in plants but there is increasing evidence for its occurrence in other organisms, including mammals. Our knowledge of the underlying mechanisms, which might involve RNA silencing, physical pairing of homologous chromosomal regions or both, is still limited. Here, we discuss the characteristics of different paramutation-like interactions in the light of arguments supporting each of these alternative mechanisms.
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Affiliation(s)
- Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands.
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23
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Wegel E, Vallejos RH, Christou P, Stöger E, Shaw P. Large-scale chromatin decondensation induced in a developmentally activated transgene locus. J Cell Sci 2005; 118:1021-31. [PMID: 15713746 DOI: 10.1242/jcs.01685] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The high molecular weight (HMW) glutenin-encoding genes in wheat are developmentally activated in the endosperm at about 8 days after anthesis. We have investigated the physical changes that occur in these genes in two transgenic lines containing about 20 and 50 copies each of the HMW glutenin genes together with their promoters. Using fluorescence in-situ hybridisation (FISH) and confocal imaging, we demonstrate that, in non-expressing tissue, each transgene locus consists of one or two highly condensed sites, which decondense into many foci upon activation of transcription in endosperm nuclei. Initiation of transcription can precede decondensation but not vice versa. We show that, in one of the lines, cytoplasmic transcript levels are high after onset of transcription but disappear by 14 days after anthesis, whereas small interfering RNAs, which indicate post-transcriptional gene silencing (PTGS), are detected at this stage. However, the transcript levels remain high at the transcription sites, most of the transgene copies are transcriptionally active and transcriptional activity in the nucleus ceases only with cell death at the end of endosperm development.
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MESH Headings
- Cell Nucleus/metabolism
- Chromatin/chemistry
- Chromatin/metabolism
- Chromatin/ultrastructure
- Cytoplasm/metabolism
- DNA/metabolism
- DNA Methylation
- DNA Primers/chemistry
- Flow Cytometry
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Gene Silencing
- Genes, Plant
- Glutens/genetics
- Image Processing, Computer-Assisted
- In Situ Hybridization
- In Situ Hybridization, Fluorescence
- Metaphase
- Microscopy, Confocal
- Plant Physiological Phenomena
- Plant Roots/metabolism
- Plants, Genetically Modified
- Plasmids/metabolism
- Promoter Regions, Genetic
- Protein Structure, Tertiary
- RNA/metabolism
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- Seeds/metabolism
- Time Factors
- Transcription, Genetic
- Transformation, Genetic
- Transgenes
- Triticum/genetics
- Triticum/metabolism
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Affiliation(s)
- Eva Wegel
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
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24
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Abstract
Eukaryotic genomes are distributed on linear chromosomes that are grouped together in the nucleus, an organelle separated from the cytoplasm by a characteristic double membrane studded with large proteinaceous pores. The chromatin within chromosomes has an as yet poorly characterized higher-order structure, but in addition to this, chromosomes and specific subchromosomal domains are nonrandomly positioned in nuclei. This review examines functional implications of the long-range organization of the genome in interphase nuclei. A rigorous test of the physiological importance of nuclear architecture is achieved by introducing mutations that compromise both structure and function. Focussing on such genetic approaches, we address general concepts of interphase nuclear order, the role of the nuclear envelope (NE) and lamins, and finally the importance of spatial organization for DNA replication and heritable gene expression.
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Affiliation(s)
- Angela Taddei
- University of Geneva, Department of Molecular Biology, CH-1211 Geneva 4, Switzerland
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25
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Somers DA, Makarevitch I. Transgene integration in plants: poking or patching holes in promiscuous genomes? Curr Opin Biotechnol 2004; 15:126-31. [PMID: 15081050 DOI: 10.1016/j.copbio.2004.02.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Transgene integration in plants transformed by either Agrobacterium or direct DNA delivery methods occurs through illegitimate recombination (IR). The precise mechanism(s) for IR-mediated transgene integration and the role of host double-strand break repair enzymes remain unknown. A recent wealth of sequenced transgene loci and investigations aimed at genetically dissecting transgene integration mechanism(s) have provided new insights into the process.
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Affiliation(s)
- David A Somers
- Department of Agronomy and Plant Genetics, Plant Molecular Genetics Institute, University of Minnesota, 1991 Upper Buford Circle, St. Paul, Minnesota, USA.
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26
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Chandler VL, Stam M. Chromatin conversations: mechanisms and implications of paramutation. Nat Rev Genet 2004; 5:532-44. [PMID: 15211355 DOI: 10.1038/nrg1378] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vicki L Chandler
- Department of Plant Sciences, 303 Forbes Building, University of Arizona, Tucson, Arizona 85721, USA.
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27
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Abstract
An RNA-based communication network appears to play a crucial role in regulating gene expression and in repressing viral and transposon sequences in plant genomes. In this article, we consider the evidence that gene expression might also be controlled epigenetically at a level other than non-coding RNA species-chromosome pairing. This epigenetic communication between sequences might be based--as it is in other organisms--on the physical pairing between homologues and the transfer of information between corresponding epigenetic landscapes. We suggest that paramutation might represent just one--albeit extreme and obvious--facet of a pairing-based gene expression regulation system in plants. Further exciting evidence for pairing occurring between homologues in plants is now mounting. An appreciation that pairing interactions might be important throughout plant development could assist in understanding phenomena such as endosperm imprinting, hybrid phenotypes and inbreeding depression.
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28
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Tessadori F, van Driel R, Fransz P. Cytogenetics as a tool to study gene regulation. TRENDS IN PLANT SCIENCE 2004; 9:147-53. [PMID: 15003238 DOI: 10.1016/j.tplants.2004.01.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Affiliation(s)
- Federico Tessadori
- Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
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29
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Abstract
An unusual feature of the Diptera is that homologous chromosomes are intimately synapsed in somatic cells. At a number of loci in Drosophila, this pairing can significantly influence gene expression. Such influences were first detected within the bithorax complex (BX-C) by E.B. Lewis, who coined the term transvection to describe them. Most cases of transvection involve the action of enhancers in trans. At several loci deletion of the promoter greatly increases this action in trans, suggesting that enhancers are normally tethered in cis by the promoter region. Transvection can also occur by the action of silencers in trans or by the spreading of position effect variegation from rearrangements having heterochromatic breakpoints to paired unrearranged chromosomes. Although not demonstrated, other cases of transvection may involve the production of joint RNAs by trans-splicing. Several cases of transvection require Zeste, a DNA-binding protein that is thought to facilitate homolog interactions by self-aggregation. Genes showing transvection can differ greatly in their response to pairing disruption. In several cases, transvection appears to require intimate synapsis of homologs. However, in at least one case (transvection of the iab-5,6,7 region of the BX-C), transvection is independent of synapsis within and surrounding the interacting gene. The latter example suggests that transvection could well occur in organisms that lack somatic pairing. In support of this, transvection-like phenomena have been described in a number of different organisms, including plants, fungi, and mammals.
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Affiliation(s)
- Ian W Duncan
- Department of Biology, Washington University, Campus Box 1229, St. Louis, Missouri 63130, USA.
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30
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Santos AP, Abranches R, Stoger E, Beven A, Viegas W, Shaw PJ. The architecture of interphase chromosomes and gene positioning are altered by changes in DNA methylation and histone acetylation. J Cell Sci 2002; 115:4597-605. [PMID: 12415004 DOI: 10.1242/jcs.00160] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wheat nuclei have a remarkably well defined interphase organisation, and we have made use of this to determine the relationship between interphase chromosome organisation, the positioning of specific transgenes and induced changes in DNA methylation and histone acetylation, using in situ hybridisation and confocal 3D imaging. After germinating seeds either in the presence of 5-Azacytidine (5-AC), which leads to DNA hypomethylation, or trichostatin A (TSA), which results in histone hyperacetylation, the architecture of the interphase chromosome arms changes significantly even though the overall Rabl configuration is maintained. This suggests that specific chromosome segments are remodelled by these treatments but that there is a strong link of both centromeres and telomeres to the nuclear envelope. In lines carrying multiple transgene integrations at widely separated sites, we show that the multiple transgenes, which are usually colocalised during interphase, are dispersed after 5-AC or TSA treatment and that there is an increase in transgene activity. This suggests that the colocalisation/dispersion of the transgenes may be a function of specific interphase chromosome organisation and that these lines containing multiple transgene copies may all be partially transcriptionally repressed.
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31
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Svitashev SK, Pawlowski WP, Makarevitch I, Plank DW, Somers DA. Complex transgene locus structures implicate multiple mechanisms for plant transgene rearrangement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 32:433-45. [PMID: 12445116 DOI: 10.1046/j.1365-313x.2002.01433.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To more fully characterize the internal structure of transgene loci and to gain further understanding of mechanisms of transgene locus formation, we sequenced more than 160 kb of complex transgene loci in two unrelated transgenic oat (Avena sativa L.) lines transformed using microprojectile bombardment. The transgene locus sequences from both lines exhibited extreme scrambling of non-contiguous transgene and genomic fragments recombined via illegitimate recombination. A perfect direct repeat of the delivered DNA, and inverted and imperfect direct repeats were detected in the same transgene locus indicating that homologous recombination and synthesis-dependent mechanism(s), respectively, were also involved in transgene locus rearrangement. The most unexpected result was the small size of the fragments of delivered and genomic DNA incorporated into the transgene loci via illegitimate recombination; 50 of the 82 delivered DNA fragments were shorter than 200 bp. Eleven transgene and genomic fragments were shorter than the DNA lengths required for Ku-mediated non-homologous end joining. Detection of these small fragments provided evidence that illegitimate recombination was most likely mediated by a synthesis-dependent strand-annealing mechanism that resulted in transgene scrambling. Taken together, these results indicate that transgene locus formation involves the concerted action of several DNA break-repair mechanisms.
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Affiliation(s)
- Sergei K Svitashev
- Department of Agronomy and Plant Genetics, Plant Molecular Genetics Institute, University of Minnesota, 411 Borlaug Hall, 1991 Buford Circle, St Paul, MN 55108, USA
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32
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Fuchs J, Lorenz A, Loidl J. Chromosome associations in budding yeast caused by integrated tandemly repeated transgenes. J Cell Sci 2002; 115:1213-20. [PMID: 11884520 DOI: 10.1242/jcs.115.6.1213] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The binding of GFP-tagged tetracycline repressor (TetR) molecules to chromosomally integrated tetracycline operator (tetO) sequence repeats has been used as a system to study chromosome behaviour microscopically in vivo. We found that these integrated transgenes influence the architecture of yeast interphase nuclei, as chromosomal loci with tandem repeats of exogenous tetO sequences are frequently associated. These associations occur only if TetR molecules are present. tetO tandem repeats associate regardless of their chromosomal context. When they are present at a proximal and a distal chromosomal position, they perturb the normal polarized Rabl-arrangement of chromosome arms by recruiting chromosome ends to the centromeric pole of the nucleus. Associations are established at G1 and are reduced during S-phase and mitosis. This system may serve as a model for the role of DNA sequence-specific binding proteins in imposing nonrandom distribution of chromosomes within the nucleus.
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Affiliation(s)
- Jörg Fuchs
- Institute of Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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33
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Twyman RM, Kohli A, Stoger E, Christou P. Foreign DNA: integration and expression in transgenic plants. GENETIC ENGINEERING 2002; 24:107-36. [PMID: 12416303 DOI: 10.1007/978-1-4615-0721-5_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Affiliation(s)
- Richard M Twyman
- Molecular Biotechnology Unit, John Innes Centre, Norwich, NR4 7UH United Kingdom
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34
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Svitashev SK, Somers DA. Genomic interspersions determine the size and complexity of transgene loci in transgenic plants produced by microprojectile bombardment. Genome 2001. [DOI: 10.1139/g01-040] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of transgene loci in six transgenic allohexaploid oat (Avena sativa L.) lines produced using microprojectile bombardment was characterized using fluorescence in situ hybridization (FISH) on extended DNA fibers (fiber-FISH). The transgene loci in five lines were composed of multiple copies of delivered DNA interspersed with genomic DNA fragments ranging in size from ca. 3 kb to at least several hundred kilobases, and in greater numbers than detected using Southern blot analysis. Although Southern analysis predicted that the transgene locus in one line consisted of long tandem repeats of the delivered DNA, fiber-FISH revealed that the locus actually contained multiple genomic interspersions. These observations indicated that transgene locus size and structure were determined by the number of transgene copies and, possibly to a greater extent, the number and the length of interspersing genomic DNA sequences within the locus. Large genomic interspersions detected in several lines were most likely the products of chromosomal breakage induced either by tissue culture conditions or, more likely, by DNA delivery into the nucleus using microprojectile bombardment. We propose that copies of transgene along with other extrachromosomal DNA fragments are used as patches to repair double-strand breaks (DSBs) in the plant genome resulting in the formation of transgene loci.Key words: genetic transformation, microprojectile bombardment, transgenic oat, FISH, transgene locus structure.
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