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1
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Koo DH, Ju Y, Putta K, Sathishraj R, Roma-Burgos N, Jugulam M, Friebe B, Gill BS. Extrachromosomal DNA-mediated glyphosate resistance in Italian ryegrass. PEST MANAGEMENT SCIENCE 2023; 79:4290-4294. [PMID: 37345512 DOI: 10.1002/ps.7626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/25/2023] [Accepted: 06/22/2023] [Indexed: 06/23/2023]
Abstract
BACKGROUND An Italian ryegrass population from Arkansas, USA developed glyphosate resistance due to 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification. The plants in this population with approximately 70 EPSPS copies were used in the present study for the physical mapping of amplified copies of EPSPS gene to determine the possible mechanism of EPSPS gene amplification conferring glyphosate resistance in Italian ryegrass. RESULT Fluorescence in situ hybridization (FISH) analysis of glyphosate resistant (GR) Italian ryegrass plants with approximately 70 EPSPS copies displayed EPSPS hybridization signals randomly on most of the metaphase chromosomes. Glyphosate susceptible (GS) Italian ryegrass plants with one EPSPS copy displayed single prominent EPSPS hybridization signal, which was co-localized with 5S rDNA locus along with few additional signals on the outside of chromosomes. Pulsed-field gel electrophoresis (PFGE) followed by DNA blot using EPSPS gene as a probe identified a prominent EPSPS hybridization around the 400 kb region in GR DNA samples, but not in GS DNA samples. CONCLUSION We report the extrachromosomal DNA-mediated glyphosate resistance in Italian ryegrass. Physical mapping of amplified copies of EPSPS gene in Italian ryegrass by FISH gives us a clue that the amplified copies of EPSPS gene may be present in the extrachromosomal DNA elements. Further analysis by PFGE followed by DNA blotting revealed that the extrachromosomal DNA containing EPSPS is approximately 400 kb similar in size with that of eccDNA replicon in Amaranthus palmeri. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Dal-Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Yoonha Ju
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Karthik Putta
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Rajendran Sathishraj
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Nilda Roma-Burgos
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
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2
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Hung KL, Luebeck J, Dehkordi SR, Colón CI, Li R, Wong ITL, Coruh C, Dharanipragada P, Lomeli SH, Weiser NE, Moriceau G, Zhang X, Bailey C, Houlahan KE, Yang W, González RC, Swanton C, Curtis C, Jamal-Hanjani M, Henssen AG, Law JA, Greenleaf WJ, Lo RS, Mischel PS, Bafna V, Chang HY. Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH. Nat Genet 2022; 54:1746-1754. [PMID: 36253572 PMCID: PMC9649439 DOI: 10.1038/s41588-022-01190-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 08/22/2022] [Indexed: 12/15/2022]
Abstract
Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agarose-entrapped genomic DNA, previously developed for bacterial chromosome segments, to isolate megabase-sized human ecDNAs. We demonstrate strong enrichment of ecDNA molecules containing EGFR, FGFR2 and MYC from human cancer cells and NRAS ecDNA from human metastatic melanoma with acquired therapeutic resistance. Targeted enrichment of ecDNA versus chromosomal DNA enabled phasing of genetic variants, identified the presence of an EGFRvIII mutation exclusively on ecDNAs and supported an excision model of ecDNA genesis in a glioblastoma model. CRISPR-CATCH followed by nanopore sequencing enabled single-molecule ecDNA methylation profiling and revealed hypomethylation of the EGFR promoter on ecDNAs. We distinguished heterogeneous ecDNA species within the same sample by size and sequence with base-pair resolution and discovered functionally specialized ecDNAs that amplify select enhancers or oncogene-coding sequences.
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Affiliation(s)
- King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Caterina I Colón
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ivy Tsz-Lo Wong
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Prashanthi Dharanipragada
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Shirley H Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Natasha E Weiser
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Xiao Zhang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kathleen E Houlahan
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenting Yang
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Rocío Chamorro González
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
- University College London Hospitals NHS Trust, London, UK
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
- University College London Hospitals NHS Trust, London, UK
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Roger S Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Paul S Mischel
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Profiling oncogenic extra-chromosomal DNA in cancer. Nat Genet 2022; 54:1591-1592. [DOI: 10.1038/s41588-022-01193-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Hung KL, Mischel PS, Chang HY. Gene regulation on extrachromosomal DNA. Nat Struct Mol Biol 2022; 29:736-744. [PMID: 35948767 PMCID: PMC10246724 DOI: 10.1038/s41594-022-00806-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022]
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) is prevalent in human cancer and is associated with poor outcomes. Clonal, megabase-sized circular ecDNAs in cancer are distinct from nonclonal, small sub-kilobase-sized DNAs that may arise during normal tissue homeostasis. ecDNAs enable profound changes in gene regulation beyond copy-number gains. An emerging principle of ecDNA regulation is the formation of ecDNA hubs: micrometer-sized nuclear structures of numerous copies of ecDNAs tethered by proteins in spatial proximity. ecDNA hubs enable cooperative and intermolecular sharing of DNA regulatory elements for potent and combinatorial gene activation. The 3D context of ecDNA shapes its gene expression potential, selection for clonal heterogeneity among ecDNAs, distribution through cell division, and reintegration into chromosomes. Technologies for studying gene regulation and structure of ecDNA are starting to answer long-held questions on the distinct rules that govern cancer genes beyond chromosomes.
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Affiliation(s)
- King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine and ChEM-H, Stanford University, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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5
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Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong ITL, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature 2021; 600:731-736. [PMID: 34819668 PMCID: PMC9126690 DOI: 10.1038/s41586-021-04116-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/08/2021] [Indexed: 02/07/2023]
Abstract
Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation1. Gene induction typically involves cis-regulatory elements that contact and activate genes on the same chromosome2,3. Here we show that ecDNA hubs-clusters of around 10-100 ecDNAs within the nucleus-enable intermolecular enhancer-gene interactions to promote oncogene overexpression. ecDNAs that encode multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumours. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the bromodomain and extraterminal domain (BET) protein BRD4 in a MYC-amplified colorectal cancer cell line. The BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-derived-oncogene transcription. The BRD4-bound PVT1 promoter is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent expression of MYC. Furthermore, the PVT1 promoter on an exogenous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic silencing of ecDNA enhancers by CRISPR interference reveals intermolecular enhancer-gene activation among multiple oncogene loci that are amplified on distinct ecDNAs. Thus, protein-tethered ecDNA hubs enable intermolecular transcriptional regulation and may serve as units of oncogene function and cooperative evolution and as potential targets for cancer therapy.
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Affiliation(s)
- King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Robert Schöpflin
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Joshua T Lange
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natasha E Weiser
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Celine Chen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Maria E Valieva
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ivy Tsz-Lo Wong
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Connor V Duffy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jun Tang
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - John C Rose
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jordan Friedlein
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Anindya Bagchi
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Stefan Mundlos
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Paul S Mischel
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Koo DH, Molin WT, Saski CA, Jiang J, Putta K, Jugulam M, Friebe B, Gill BS. Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeri. Proc Natl Acad Sci U S A 2018; 115:3332-3337. [PMID: 29531028 PMCID: PMC5879691 DOI: 10.1073/pnas.1719354115] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Gene amplification has been observed in many bacteria and eukaryotes as a response to various selective pressures, such as antibiotics, cytotoxic drugs, pesticides, herbicides, and other stressful environmental conditions. An increase in gene copy number is often found as extrachromosomal elements that usually contain autonomously replicating extrachromosomal circular DNA molecules (eccDNAs). Amaranthus palmeri, a crop weed, can develop herbicide resistance to glyphosate [N-(phosphonomethyl) glycine] by amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, the molecular target of glyphosate. However, biological questions regarding the source of the amplified EPSPS, the nature of the amplified DNA structures, and mechanisms responsible for maintaining this gene amplification in cells and their inheritance remain unknown. Here, we report that amplified EPSPS copies in glyphosate-resistant (GR) A. palmeri are present in the form of eccDNAs with various conformations. The eccDNAs are transmitted during cell division in mitosis and meiosis to the soma and germ cells and the progeny by an as yet unknown mechanism of tethering to mitotic and meiotic chromosomes. We propose that eccDNAs are one of the components of McClintock's postulated innate systems [McClintock B (1978) Stadler Genetics Symposium] that can rapidly produce soma variation, amplify EPSPS genes in the sporophyte that are transmitted to germ cells, and modulate rapid glyphosate resistance through genome plasticity and adaptive evolution.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - William T Molin
- Crop Production Systems Research Unit, US Department of Agriculture-Agricultural Research Services, Stoneville, MS 38776
| | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Karthik Putta
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Bernd Friebe
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506;
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Berent LM, Messick JB. Physical map and genome sequencing survey of Mycoplasma haemofelis (Haemobartonella felis). Infect Immun 2003; 71:3657-62. [PMID: 12761157 PMCID: PMC155732 DOI: 10.1128/iai.71.6.3657-3662.2003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma haemofelis is an uncultivable red-cell pathogen of cats. Isolated M. haemofelis DNA was used to create a bacterial artificial chromosome library and physical map. Random sequencing of this material revealed 75 genes that had not been previously reported for M. haemofelis or any other hemotrophic mycoplasma.
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Affiliation(s)
- Linda M Berent
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana 61802, USA
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Lundin C, Schultz N, Arnaudeau C, Mohindra A, Hansen LT, Helleday T. RAD51 is involved in repair of damage associated with DNA replication in mammalian cells. J Mol Biol 2003; 328:521-35. [PMID: 12706714 DOI: 10.1016/s0022-2836(03)00313-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The RAD51 protein, a eukaryotic homologue of the Escherichia coli RecA protein, plays an important role in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) in mammalian cells. Recent findings suggest that HR may be important in repair following replication arrest in mammalian cells. Here, we have investigated the role of RAD51 in the repair of different types of damage induced during DNA replication with etoposide, hydroxyurea or thymidine. We show that etoposide induces DSBs at newly replicated DNA more frequently than gamma-rays, and that these DSBs are different from those induced by hydroxyurea. No DSB was found following treatment with thymidine. Although these compounds appear to induce different DNA lesions during DNA replication, we show that a cell line overexpressing RAD51 is resistant to all of them, indicating that RAD51 is involved in repair of a wide range of DNA lesions during DNA replication. We observe fewer etoposide-induced DSBs in RAD51-overexpressing cells and that HR repair of etoposide-induced DSBs is faster. Finally, we show that induced long-tract HR in the hprt gene is suppressed in RAD51-overexpressing cells, although global HR appears not to be suppressed. This suggests that overexpression of RAD51 prevents long-tract HR occurring during DNA replication. We discuss our results in light of recent models suggested for HR at stalled replication forks.
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Affiliation(s)
- Cecilia Lundin
- Department of Genetic and Cellular Toxicology, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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9
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Lundin C, Erixon K, Arnaudeau C, Schultz N, Jenssen D, Meuth M, Helleday T. Different roles for nonhomologous end joining and homologous recombination following replication arrest in mammalian cells. Mol Cell Biol 2002; 22:5869-78. [PMID: 12138197 PMCID: PMC133974 DOI: 10.1128/mcb.22.16.5869-5878.2002] [Citation(s) in RCA: 189] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Homologous recombination (HR) and nonhomologous end joining (NHEJ) play overlapping roles in repair of DNA double-strand breaks (DSBs) generated during the S phase of the cell cycle. Here, we characterized the involvement of HR and NHEJ in the rescue of DNA replication forks arrested or slowed by treatment of hamster cells with hydroxyurea or thymidine. We show that the arrest of replication with hydroxyurea generates DNA fragmentation as a consequence of the formation of DSBs at newly replicated DNA. Both HR and NHEJ protected cells from the lethal effects of hydroxyurea, and this agent also increased the frequency of recombination mediated by both homologous and nonhomologous exchanges. Thymidine induced a less stringent arrest of replication and did not generate detectable DSBs. HR alone rescued cells from the lethal effects of thymidine. Furthermore, thymidine increased the frequency of DNA exchange mediated solely by HR in the absence of detectable DSBs. Our data suggest that both NHEJ and HR are involved in repair of arrested replication forks that include a DSB, while HR alone is required for the repair of slowed replication forks in the absence of detectable DSBs.
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Affiliation(s)
- Cecilia Lundin
- Department of Genetic and Cellular Toxicology, Stockholm University, S-106 91 Stockholm, Sweden
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10
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Gao Y, Lu YJ, Xue SA, Chen H, Wedderburn N, Griffin BE. Hypothesis: a novel route for immortalization of epithelial cells by Epstein-Barr virus. Oncogene 2002; 21:825-35. [PMID: 11850810 DOI: 10.1038/sj.onc.1205130] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2001] [Revised: 10/30/2001] [Accepted: 10/31/2001] [Indexed: 11/09/2022]
Abstract
Transfection of primate tissue explants with a specific sub-fragment (p31) of EBV DNA results in epithelial (but no other) cells proliferating indefinitely (becoming 'immortalized') without evidence of a 'growth crisis'. Molecular evidence supports integration of viral information into the host chromosome, and an early genotypic alteration involving specific amplification of a sub-component (IR1) of p31 DNA, followed by apparent loss of viral DNA from chromosomes, consistent with a 'hit and run' mechanism. However, analysis at the individual cell level during long-term culture, by FISH techniques, reveals chromosomal alterations, and viral sequences surviving within double minute (DM) bodies. Changing growth patterns occurring at different stages during propagation (>a year in culture) may be explained by sporadic reintegration of surviving viral DNA into the host chromosome. Notably, throughout culture, telomere lengths in chromosomal DNAs do not alter but rather retain the length observed in the primary cell populations. Introduction of a growth stimulating function of EBV, BARF1, into the immortalized, non-clonable epithelial cells under conditions which permit overexpression, allows clonal populations to be derived. Based on the data, mechanisms of immortalization, in the absence of a proven viral oncogene in p31 DNA, and possible genes involved, are considered.
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Affiliation(s)
- Yanning Gao
- Viral Oncology Unit, Department of Medicine, Imperial College of Science, Technology and Medicine, Norfolk Place, London W2 1PG, UK
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Amils R, Irazabal N, Moreira D, Abad JP, Marín I. Genomic organization analysis of acidophilic chemolithotrophic bacteria using pulsed field gel electrophoretic techniques. Biochimie 1998; 80:911-21. [PMID: 9893951 DOI: 10.1016/s0300-9084(00)88888-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The genomic organization of acidophilic chemolithotrophic bacteria belonging to the genus Thiobacillus, Thiomonas and Leptospirillum was studied using pulsed field gel electrophoresis techniques (PFGE). The electrophoretic analysis of intact DNA prepared from different strains showed that all have a circular chromosome, with sizes ranging from 1.9 Mb for Leptospirillum ferrooxidans ATCC 49879, the smallest genome for an acidophilic strict chemolithoautotrophic microorganism, to 3.8 Mb for Thiomonas cuprina DSM 5495, the largest in this study. The number of extrachromosomal elements present varied from none, as observed in several isolates of Leptospirillum ferrooxidan, to five in Thiobacillus thiooxidans ATCC 8085. The mixotroph Thiomonas cuprina DSM 5495 was found to have a linear 50 kb megaplasmid which was inducible when the bacteria was grown in chemolithotrophic conditions. Low-frequency restriction fragment analysis (LFRFA) of different acidophilic chemolithotrophs and related species was carried out by PFGE to determine macrorestriction patterns for rare cutters (SpeI, XbaI, SwaI, PmeI), which were then used for taxonomic identification (karyotyping), genome size determination, and generation of physical and genetic maps.
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Affiliation(s)
- R Amils
- Centro de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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12
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Kuo MT, Sen S, Hittelman WN, Hsu TC. Chromosomal fragile sites and DNA amplification in drug-resistant cells. Biochem Pharmacol 1998; 56:7-13. [PMID: 9698083 DOI: 10.1016/s0006-2952(98)00040-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
It has been well established that DNA amplification is one of the important mechanisms by which cultured cells acquire resistance to many cytotoxic compounds. Amplification of important genes including those encoding oncoproteins, growth factors, their receptors and cell-cycle regulators has been reported in human neoplasms. Yet, despite intensive research since the first description of DNA amplification in cultured cells about 20 years ago, the mechanisms of DNA amplification remain largely unknown. Many models have been proposed to account for the diverse manifestations of amplified DNA in many different cell sources. It is not the intention of this commentary to review these many different models. Rather, we wil focus on the recent advances in this area of research, made mainly via the fluorescence in situ hybridization technique, that have revealed a fairly common chromosomal manifestation of amplified DNA in the drug-resistant hamster cell lines and have demonstrated the association of chromosomal fragile site breakage with early events in DNA amplification. These new developments underscore the importance of future research toward understanding the molecular bases of chromosomal fragile sites, including mechanisms involved in DNA strand breakage and repair, chromosomal translocations, and deletions, which may, in turn, provide important new insights into genomic plasticity and neoplastic transformation.
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Affiliation(s)
- M T Kuo
- Department of Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, Houston 77030, USA.
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13
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Marín I, Amils R, Abad JP. Genomic organization of the metal-mobilizing bacterium Thiobacillus cuprinus. Gene X 1997; 187:99-105. [PMID: 9073072 DOI: 10.1016/s0378-1119(96)00731-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The genomic organization of Thiobacillus cuprinus, a facultative chemolithotrophic bacterium that preferentially solubilizes copper from complex ores, has been studied by Pulsed Field Gel Electrophoresis (PFGE). It has been determined that T. cuprinus has a circular chromosome of about 3.8 Mb in size as concluded by analysis of gamma-irradiated total DNA and restriction analysis. Macrorestriction patterns for several restriction enzymes have been generated. Restriction enzymes AseI, DraI, SpeI, SwaI and XbaI give a number of fragments that can be adequately resolved by PFGE and then be used for electrophoretic karyotyping and for the construction of physical maps of the chromosome. Such a map has been constructed for the endonucleases SpeI and SwaI. The localization of several heterologous and homologous genes on the physical map, including those for rRNA, has paved the way for the construction of a genetic map.
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Affiliation(s)
- I Marín
- Centro de Biología Molecular Severo Ochoa (C.S.I.C.-U.A.M.), Universidad Autonóma de Madrid, Cantoblanco, Spain
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14
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Cedervall B, Radivoyevitch T. Methods for analysis of DNA fragment distributions on pulsed field gel electrophoretic gels. Electrophoresis 1996; 17:1080-6. [PMID: 8832175 DOI: 10.1002/elps.1150170617] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- B Cedervall
- Department of Medical Radiobiology, Karolinska Institutet, Stockholm, Sweden
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15
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Eijdems EW, De Haas M, Coco-Martin JM, Ottenheim CP, Zaman GJ, Dauwerse HG, Breuning MH, Twentyman PR, Borst P, Baas F. Mechanisms of MRP over-expression in four human lung-cancer cell lines and analysis of the MRP amplicon. Int J Cancer 1995; 60:676-84. [PMID: 7860142 DOI: 10.1002/ijc.2910600518] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Some multidrug resistant cell lines over-express the gene encoding the multidrug-resistance-associated protein (MRP). In all cell lines reported thus far, over-expression is associated with gene amplification. We have studied the predominant mechanisms of MRP over-expression in 4 human lung-cancer cell lines that cover a range of drug-resistance levels, and we have analyzed the MRP amplicon. In the SW-1573-derived, weakly resistant cell line 30.3M, MRP mRNA is elevated 3-fold in the absence of gene amplification. Run-on analysis shows that the increased MRP gene expression in this cell line is due to transcriptional activation. In the highly resistant GLC4/ADR and COR-L23/R cells, MRP gene amplification predominates, whereas in the moderately resistant MOR/R cells, gene amplification is combined with a mechanism resulting in an additional increase in the level of MRP mRNA. Fluorescence in situ hybridization shows that, in the GLC4/ADR cells, amplified MRP sequences are present both in double minute chromosomes (DM) and in homogeneously staining regions (HSR). By pulsed-field gel electrophoresis we show that the MRP-containing DM are 1 Mb in length. Chromosome-16-specific repetitive sequences adjacent to the MRP gene are also present in the DM and HSR, compatible with the involvement of these sequences in recombination events underlying MRP gene amplification. Our results show that low levels of drug resistance may arise by transcriptional activation of the MRP gene, whereas at high levels of drug resistance amplification of the MRP gene predominates, possibly facilitated by the presence of recombination-prone sequences.
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MESH Headings
- ATP-Binding Cassette Transporters/biosynthesis
- ATP-Binding Cassette Transporters/genetics
- Antineoplastic Agents/pharmacology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Small Cell/genetics
- Carcinoma, Small Cell/metabolism
- Carcinoma, Small Cell/pathology
- Chromosomes, Human, Pair 16
- DNA, Complementary/genetics
- DNA, Neoplasm/genetics
- Drug Resistance, Multiple/genetics
- Gene Amplification
- Gene Expression Regulation, Neoplastic
- Genes
- Humans
- In Situ Hybridization, Fluorescence
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Multidrug Resistance-Associated Proteins
- Myosins/biosynthesis
- Myosins/genetics
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- RNA, Messenger/genetics
- RNA, Neoplasm/genetics
- Recombination, Genetic
- Repetitive Sequences, Nucleic Acid
- Tumor Cells, Cultured/drug effects
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Affiliation(s)
- E W Eijdems
- Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam
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16
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Abstract
Macrorestriction fragment analysis of DNA from Pseudomonas cepacia 17616, in conjunction with Southern hybridization experiments using junction fragments containing rare restriction enzyme sites as probes, indicated that this bacterium contains three large circular replicons of 3.4, 2.5, and 0.9 megabases (Mb). Inclusion of the 170-kb cryptic plasmid present in this strain gave an overall estimate of genome size of 7 Mb. Other Southern hybridization experiments indicated that the three large replicons contained rRNA genes as well as insertion sequence elements identified previously in this strain. The distribution of SwaI, PacI, and PmeI sites on the three replicons was determined. A derivative of Tn5-751 carrying a SwaI site was used to inactivate and map genes on the 2.5- and 3.4-Mb replicons. Mutants were isolated in which the 2.5- and 0.9-Mb replicons had been reduced in size to 1.8 and 0.65 Mb, respectively. The loss of DNA from the 2.5-Mb replicon was associated with lysine auxotrophy, beta-lactamase deficiency, and failure to utilize ribitol and trehalose as carbon and energy sources. DNA fragments corresponding in size to randomly linearized forms of the different replicons were detected in unrestricted DNA by pulsed-field gel electrophoresis. The results provide a framework for further genetic analysis of strain 17616 and for evaluation of the genomic complexities of other P. cepacia isolates.
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Affiliation(s)
- H P Cheng
- Department of Microbiology, University of Massachusetts, Amherst 01002
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17
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Sognier MA, McCombs J, Brown DB, Lynch G, Tucker M, Eberle R, Belli JA. Use of chromosome microdissection, the polymerase chain reaction, and dot blot hybridization to analyze double minute chromosomes. GENETIC ANALYSIS, TECHNIQUES AND APPLICATIONS 1994; 11:69-76. [PMID: 7803132 DOI: 10.1016/1050-3862(94)90053-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The potential usefulness of chromosome microdissection, the polymerase chain reaction (PCR), and dot blot hybridization as a quick screening method for determining the genetic composition of double minute chromosomes (DMs) was evaluated. DMs or abnormally banding regions (ABRs) were microdissected from multidrug-resistant hamster cell lines and amplified with PCR using primers specific for the hamster multidrug-resistance (MDR) gene, pgp 1. The microdissected-PCR-amplified products were shown to (a) hybridize to a 32P-labeled pCHP1 probe for the hamster MDR gene by using dot blot or Southern blot analysis and also (b) hybridize back to the chromosome region from which they were originally dissected by using fluorescent in situ hybridization. Microdissected/PCR-amplified DMs were also shown to hybridize to ABRs. When microdissected DMs and ABRs were amplified using hamster specific Alu primers, the resulting material was shown to hybridize with probes for hamster MDR and Alu. These results suggest that the DMs contained in these MDR hamster cell lines contain Alu-like sequences and the chromosome microdissection-PCR-hybridization approach might be used as a quick screening method for identifying genes amplified in DMs and ABRs in cell lines and human tumor samples.
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Affiliation(s)
- M A Sognier
- University of Texas Medical Branch, Department of Radiation Therapy, Galveston 77555
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18
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Papadopoulou B, Roy G, Ouellette M. Frequent amplification of a short chain dehydrogenase gene as part of circular and linear amplicons in methotrexate resistant Leishmania. Nucleic Acids Res 1993; 21:4305-12. [PMID: 8414986 PMCID: PMC310065 DOI: 10.1093/nar/21.18.4305] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The H locus of Leishmania codes for a short chain dehydrogenase gene (ltdh) that is involved in antifolate resistance. Leishmania tarentolae cells, selected in a step by step fashion for resistance to the antifolate methotrexate (MTX), frequently amplified ltdh in response to drug selection. Both circular and linear extrachromosomal amplicons were generated de novo from the chromosomal H locus and several contained inverted duplications. At least four different rearrangement points were used during the formation of amplicons, with one of them used preferentially. All mutants highly resistant to MTX, whether or not they have the H locus amplified, showed a decreased steady-state accumulation of MTX. Nevertheless, two types of transport mutants were clearly discernable. In the first type, accumulation was reduced four to five-fold, whereas in the second class of mutants, accumulation was reduced more than 50-fold. The ltdh gene was amplified in all the mutants with the transport mutation of the first type, but not in all the mutants with a more pronounced decrease in the steady-state accumulation of MTX. Both types of transport mutation, leading to the reduction in MTX accumulation, arose early during the selection process and were stable even when cells were grown in absence of the drug for prolonged period.
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Affiliation(s)
- B Papadopoulou
- Centre de Recherche du CHUL, Faculté de Médecine, Université Laval, Québec, Canada
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19
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Abstract
Double-minute chromosomes play a critical role in tumor cell genetics where they are frequently associated with the overexpression of oncogene products. They have been observed for many years in light microscopic examinations of metaphase chromosomes from tumor cells, but their origin remains unknown and is the subject of considerable speculation. However, molecular details of their structure and organization can now be described in conjunction with the microscopic examinations, to allow an evaluation of the various models that have been developed to explain the genesis of double-minutes. The evidence now favors simple models that invoke chromosome breakage and circularization of very large acentric chromosome fragments, permitting unequal segregation of the genes on the fragment during cell division. If there is selection for overexpression of one of the genes on the fragment, daughter cells with more fragments will grow faster than daughter cells with fewer fragments, and over time the population of cells will come to contain many double-minutes per cell.
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Affiliation(s)
- P J Hahn
- Department of Radiology, State University of New York Health Science Center, Syracuse
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20
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Abstract
The DNA sequences that are necessary for the formation of a functional mammalian chromosome are thought to be the origins of replication, the telomeres and the centromere. Telomere structure is now well understood, with the functional element characterized as the motif (TTAGGG)n. The structures of the DNA regions that contain origins of replication and a centromere are known, but the functionally important elements within these regions are still only poorly defined.
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Affiliation(s)
- C Tyler-Smith
- Department of Biochemistry, University of Oxford, UK
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21
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VanDevanter DR, Yirdaw G. Recombination between separate MYC amplification structures in COLO320 cells. Genes Chromosomes Cancer 1993; 6:190-7. [PMID: 7682105 DOI: 10.1002/gcc.2870060310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cytogenetically visible gene amplification structures can consist of arrays of amplicons presumably formed by secondary "rearrangements" following amplicon formation. The structural evolution of gene amplification sites in tumor cells suggests that complex secondary structures may have some selective advantage in the tumor cell environment. Although secondary amplicon rearrangements are a hallmark of the gene amplification process, little is known about the mechanics of this process. COLO320 neuroendocrine tumor cells carry two different types of amplified MYC oncogene sequences, one type with an intact MYC gene and the other with a rearranged "chimeric" MYC gene. We have studied various clonal subpopulations of COLO320 cells and identified regions within and downstream of the MYC locus that are unique to each amplicon type. Using double-label fluorescence in situ hybridization with DNA probes unique to each amplicon type, we have observed that both chromosomal and extrachromosomal MYC amplicon arrays in COLO320 cells frequently consist of heterogeneous mixtures of each MYC amplicon type. Our results suggest that the two MYC amplicon types of COLO320 cells were formed simultaneously but independently, and that double minute chromosomes observed in COLO320 cells were formed by intermolecular homologous recombination secondary to amplicon formation.
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22
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Nonet GH, Wahl GM. Introduction of YACs containing a putative mammalian replication origin into mammalian cells can generate structures that replicate autonomously. SOMATIC CELL AND MOLECULAR GENETICS 1993; 19:171-92. [PMID: 8511674 DOI: 10.1007/bf01233532] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Yeast artificial chromosomes (YACs) containing or lacking a biochemically defined DNA replication origin were transferred from yeast to mammalian cells in order to determine whether origin-dependent autonomous replication would occur. A specialized YAC vector was designed to enable selection for YACs in mammalian cells and for monitoring YAC abundance in individual mammalian cells. All of eight clones made with linear and circularized YACs lacking the origin and seven of nine clones made with linear and circularized YACs containing the origin region contained single copies of the transfected YAC, along with various amounts of yeast DNA, integrated into single but different chromosomal sites. By contrast, two transformants derived from circularized YACs containing the putative replication origin showed very heterogeneous YAC copy number and numerous integration sites when analyzed after many generations of in vitro propagation. Analysis of both clones at an early time after fusion revealed variously sized extrachromosomal YAC/yeast structures reminiscent of the extrachromosomal elements found in some cells harboring amplified genes. The data are consistent with the interpretation that YACs containing a biochemically defined origin of replication can initially replicate autonomously, followed by integration into multiple chromosomal locations, as has been reported to occur in many examples of gene amplification in mammalian cells.
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Affiliation(s)
- G H Nonet
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
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23
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Neimark H, Kirkpatrick BC. Isolation and characterization of full-length chromosomes from non-culturable plant-pathogenic Mycoplasma-like organisms. Mol Microbiol 1993; 7:21-8. [PMID: 7679771 DOI: 10.1111/j.1365-2958.1993.tb01093.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We describe the isolation and characterization of full-length chromosomes from non-culturable plant-pathogenic, mycoplasma-like organisms (MLOs). MLO chromosomes are circular and their sizes (640 to 1185 kbp) are heterogeneous. Divergence in the range of chromosome sizes is apparent between MLOs in the two major MLO disease groups, and chromosome size polymorphism occurs among some related agents. MLO chromosome sizes overlap those of culturable mycoplasmas; consequently, small genome size alone cannot explain MLO non-culturability. Hybridization with cloned MLO-specific chromosomal and 16S rRNA probes detected two separate chromosomes in some MLO 'type' strains. Large DNA molecules that appear to be MLO megaplasmids were also demonstrated. The ability to characterize full-length chromosomes from virtually any non-culturable prokaryote should greatly facilitate the molecular and genetic analysis of these difficult bacteria.
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Affiliation(s)
- H Neimark
- Department of Microbiology and Immunology, Morse Institute for Molecular Biology, State University of New York, Brooklyn 11203
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24
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Schoenlein PV, Shen DW, Barrett JT, Pastan I, Gottesman MM. Double minute chromosomes carrying the human multidrug resistance 1 and 2 genes are generated from the dimerization of submicroscopic circular DNAs in colchicine-selected KB carcinoma cells. Mol Biol Cell 1992; 3:507-20. [PMID: 1611154 PMCID: PMC275604 DOI: 10.1091/mbc.3.5.507] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
This study characterizes amplified structures carrying the human multidrug resistance (MDR) genes in colchicine-selected multidrug resistant KB cell lines and strongly supports a model of gene amplification in which small circular extrachromosomal DNA elements generated from contiguous chromosomal DNA regions multimerize to form cytologically detectable double minute chromosomes (DMs). The human MDR1 gene encodes the 170-kDa P-glycoprotein, which is a plasma membrane pump for many structurally unrelated chemotherapeutic drugs. MDR1 and its homolog, MDR2, undergo amplification when KB cells are subjected to stepwise selection in increasing concentrations of colchicine. The structure of the amplification unit at each step of drug selection was characterized using both high-voltage gel electrophoresis and pulsed-field gel electrophoresis (PFGE) techniques. An 890-kb submicroscopic extrachromosomal circular DNA element carrying the MDR1 and MDR2 genes was detected in cell line KB-ChR-8-5-11, the earliest step in drug selection in which conventional Southern/hybridization analyses detected MDR gene amplification. When KB-ChR-8-5-11 was subjected to stepwise increases in colchicine, this circular DNA element dimerized as detected by PFGE with and without digestion with Not 1, which linearizes the 890-kb amplicon. This dimerization process, which also occurred at the next step of colchicine selection, resulted in the formation of cytologically detectable DMs revealed by analysis of Giemsa-stained metaphase spreads.
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Affiliation(s)
- P V Schoenlein
- Laboratory of Cell Biology, National Institutes of Health, National Cancer Institute, Bethesda, Maryland 20892
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25
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Amplicon structure in multidrug-resistant murine cells: a nonrearranged region of genomic DNA corresponding to large circular DNA. Mol Cell Biol 1992. [PMID: 1545798 DOI: 10.1128/mcb.12.3.1179] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug resistance (MDR) in tumor cell lines is frequently correlated with amplification of one or more mdr genes. Usually the amplified domain also includes several neighboring genes. Using pulsed-field gel electrophoresis, we have established a restriction map covering approximately 2,200 kb in the drug-sensitive mouse tumor cell line TC13K. The mapped region is located on mouse chromosome 5 and includes the three mdr genes, the gene for the calcium-binding sorcin protein, and a gene with unknown function designated class 5. Long-range maps of the amplified DNA sequences in five of six MDR sublines that had been independently derived from TC13K generally displayed the same pattern as did the parental cell line. All six MDR sublines exhibited numerous double minutes, and one of them displayed a homogeneously staining region in a subpopulation. Large circular molecules, most likely identical to one chromatid of the double minutes, were detected in four of the sublines by linearization with gamma irradiation. The size of the circles was about 2,500 kb, which correlated to a single unit of the amplified domain. We therefore propose that in four independent instances of MDR development, a single unit of about 2,500 kb has been amplified in the form of circular DNA molecules. The restriction enzyme map of the amplified unit is unchanged compared with that of the parental cell line, whereas the joining sites of the circular DNA molecules are not identical but are in the same region.
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26
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Ståhl F, Wettergren Y, Levan G. Amplicon structure in multidrug-resistant murine cells: a nonrearranged region of genomic DNA corresponding to large circular DNA. Mol Cell Biol 1992; 12:1179-87. [PMID: 1545798 PMCID: PMC369548 DOI: 10.1128/mcb.12.3.1179-1187.1992] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Multidrug resistance (MDR) in tumor cell lines is frequently correlated with amplification of one or more mdr genes. Usually the amplified domain also includes several neighboring genes. Using pulsed-field gel electrophoresis, we have established a restriction map covering approximately 2,200 kb in the drug-sensitive mouse tumor cell line TC13K. The mapped region is located on mouse chromosome 5 and includes the three mdr genes, the gene for the calcium-binding sorcin protein, and a gene with unknown function designated class 5. Long-range maps of the amplified DNA sequences in five of six MDR sublines that had been independently derived from TC13K generally displayed the same pattern as did the parental cell line. All six MDR sublines exhibited numerous double minutes, and one of them displayed a homogeneously staining region in a subpopulation. Large circular molecules, most likely identical to one chromatid of the double minutes, were detected in four of the sublines by linearization with gamma irradiation. The size of the circles was about 2,500 kb, which correlated to a single unit of the amplified domain. We therefore propose that in four independent instances of MDR development, a single unit of about 2,500 kb has been amplified in the form of circular DNA molecules. The restriction enzyme map of the amplified unit is unchanged compared with that of the parental cell line, whereas the joining sites of the circular DNA molecules are not identical but are in the same region.
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Affiliation(s)
- F Ståhl
- Department of Genetics, University of Gothenburg, Sweden
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27
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Abstract
Extrachromosomal elements are common early intermediates of gene amplification in vivo and in cell culture. The time at which several extrachromosomal elements replicate was compared with that of the corresponding amplified or unamplified chromosomal sequences. The replication timing analysis employed a retroactive synchrony method in which fluorescence-activated cell sorting was used to obtain cells at different stages of the cell cycle. Extrachromosomally amplified Syrian hamster CAD genes (CAD is an acronym for the single gene which encodes the trifunctional protein which catalyzes the first three steps of uridine biosynthesis) replicated in a narrow window of early S-phase which was approximately the same as that of chromosomally amplified CAD genes. Similarly, extrachromosomally amplified mouse adenosine deaminase genes replicated at a discrete time in early S-phase which approximated the replication time of the unamplified adenosine deaminase gene. In contrast, the multicopy extrachromosomal Epstein-Barr virus genome replicated within a narrow window in late S-phase in latently infected human Rajii cells. The data indicate that localization within a chromosome is not required for the maintenance of replication timing control.
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28
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Carroll SM, Trotter J, Wahl GM. Replication timing control can be maintained in extrachromosomally amplified genes. Mol Cell Biol 1991; 11:4779-85. [PMID: 1678857 PMCID: PMC361380 DOI: 10.1128/mcb.11.9.4779-4785.1991] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Extrachromosomal elements are common early intermediates of gene amplification in vivo and in cell culture. The time at which several extrachromosomal elements replicate was compared with that of the corresponding amplified or unamplified chromosomal sequences. The replication timing analysis employed a retroactive synchrony method in which fluorescence-activated cell sorting was used to obtain cells at different stages of the cell cycle. Extrachromosomally amplified Syrian hamster CAD genes (CAD is an acronym for the single gene which encodes the trifunctional protein which catalyzes the first three steps of uridine biosynthesis) replicated in a narrow window of early S-phase which was approximately the same as that of chromosomally amplified CAD genes. Similarly, extrachromosomally amplified mouse adenosine deaminase genes replicated at a discrete time in early S-phase which approximated the replication time of the unamplified adenosine deaminase gene. In contrast, the multicopy extrachromosomal Epstein-Barr virus genome replicated within a narrow window in late S-phase in latently infected human Rajii cells. The data indicate that localization within a chromosome is not required for the maintenance of replication timing control.
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Affiliation(s)
- S M Carroll
- Salk Institute for Biological Studies, La Jolla, California 92037
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29
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Ahn SY, Nevaldine B, Hahn PJ. Direct measurement by pulsed-field gel electrophoresis of induction and rejoining of X-ray-induced double-strand breaks in cultured mouse cells. Int J Radiat Biol 1991; 59:661-75. [PMID: 1672356 DOI: 10.1080/09553009114550591] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The induction and rejoining of X-ray-induced double-strand breaks (dsb) in chromosomal DNA has been difficult to measure. We have developed a pulsed-field gel electrophoresis (PFGE)-based system for directly estimating DNA sizes between 0.2 and 10 million base pairs. With this system we can estimate average DNA sizes from randomly broken chromosomes by measuring the approximate molecular weight of the maximum DNA concentration. In practice this is effective where the average is between 1 and 4 million bp allowing both shoulders of the distribution to be observed. This corresponds to a dose range of 20-80 Gy. Qualitative differences from non-irradiated DNA can be observed down to about 5 Gy. We have confirmed the dose response by utilizing methotrexate-resistant mouse cells containing circular double-minute (dm) chromosomes of 1, 1.5, and 3 million bp. The kinetics of dsb rejoining from doses of 50 and 5 Gy was investigated: 50 Gy reduced the chromosomal DNA to an average size of approximately 1 million bp, followed by a constant repair rate of 44 dsb per minute per cell for 3 h (assuming a total genome size of 10 million bp).
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Affiliation(s)
- S Y Ahn
- Department of Pharmacy, EWHA Women's University, Seoul, Korea
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30
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Abstract
An overview of our present understanding of mechanisms of resistance against cytotoxic drugs is presented. Most of this understanding has come from studies on tumor cells made resistant in vitro, but there is reason to think that similar mechanisms are responsible for resistance in patients. After a brief overview of biochemical mechanisms of drug resistance, the types of mutations in tumor cells that can alter drug handling are discussed. Three examples of resistance are analysed in more detail: resistance to the folate analogue methotrexate; the multidrug resistance caused by increased levels of P-glycoprotein, which extrudes drugs from the cell; and resistance to alkylating agents.
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Affiliation(s)
- P Borst
- The Netherlands Cancer Institute, Amsterdam
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31
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Dolf G, Meyn RE, Curley D, Prather N, Story MD, Boman BM, Siciliano MJ, Hewitt RR. Extrachromosomal amplification of the epidermal growth factor receptor gene in a human colon carcinoma cell line. Genes Chromosomes Cancer 1991; 3:48-54. [PMID: 2069908 DOI: 10.1002/gcc.2870030109] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In situ hybridization, using a biotinylated cDNA probe for the epidermal growth factor receptor (EGFR) gene, indicates that the amplified EGFR genes in the colon tumor cell line, DiFi, are localized in many small double minute chromosomes (dmin) of varying size and visibility. Analysis of the electrophoretic mobility of gamma-irradiated DNA from DiFi by pulsed-field gel electrophoresis and Southern blot hybridization using EGFR probe, indicates that the amplified EGFR in DiFi exists in extrachromosomal, covalently closed circular episomes, presumably equivalent to dmin. Two major and one minor species were observed which had estimated sizes of 650, 1,300, and 2,000 kb, respectively. The DiFi cell line appears to represent a unique case of extrachromosomal EGFR gene amplification in human cells.
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Affiliation(s)
- G Dolf
- Department of Molecular Genetics, University of Texas M.D. Anderson Cancer Center, Houston
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32
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33
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Use of pulsed-field gel electrophoresis to study the chromosomes of Saccharomyces and other yeasts. Methods 1990. [DOI: 10.1016/s1046-2023(05)80132-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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34
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Lin CC, Meyne J, Sasi R, Moyzis RK. Apparent lack of telomere sequences on double minute chromosomes. CANCER GENETICS AND CYTOGENETICS 1990; 48:271-4. [PMID: 2397458 DOI: 10.1016/0165-4608(90)90131-s] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- C C Lin
- Department of Pathology and Laboratory Medicine, University of Alberta, Edmonton, Canada
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35
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Hahn P, Nevaldine B, Morgan WF. X-ray induction of methotrexate resistance due to dhfr gene amplification. SOMATIC CELL AND MOLECULAR GENETICS 1990; 16:413-23. [PMID: 2122527 DOI: 10.1007/bf01233191] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The effect of ionizing radiation on methotrexate (MTX) resistance and gene amplification in cultured mammalian cells was investigated. X-irradiation of mouse EMT-6 cells induced cell killing and MTX resistance due to amplification of dihydrofolate reductase (dhfr) gene in a dose-dependent manner. The highest yields of mutant cells were obtained at approximately D37 (the dose at which 37% of the cells survive), where the frequency of MTX-resistant cells was four- to eightfold over that of the unirradiated population. The proportion of MTX-resistant cells among the survivors increased logarithmically with dose, up to a 1000-fold increase over unirradiated cells at 1000 cGy, the highest dose tested. The induced frequency of MTX resistance after X-irradiation was greater than the induced frequency of 8-azaguanine resistance, which indicates deletion of the hypoxanthine phosphoribosyltransferase gene. Inhibition of poly(ADP-ribose) polymerase by the addition of 3-aminobenzamide before irradiation increased both cell killing and MTX resistance. Metaphase spreads of chromosomes from EMT-6 cells that had been irradiated and subjected to stepwise increases in MTX concentration showed numerous double minutes. Pulsed-field gel electrophoresis of the DNA from cells containing radiation-induced double minutes showed that many copies of the dhfr gene were present on circular DNA molecules of 10(6), 2 x 10(6), and 3 x 10(6) base pairs. These results suggest a relationship between the induction of chromosome aberrations and the induction of gene amplification.
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Affiliation(s)
- P Hahn
- Department of Radiology, State University of New York Health Science Center, Syracuse 13210
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36
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Abstract
Acentric extrachromosomal elements, such as submicroscopic autonomously replicating circular molecules (episomes) and double minute chromosomes, are common early, and in some cases initial, intermediates of gene amplification in many drug-resistant and tumor cell lines. In order to gain a more complete understanding of the amplification process, we investigated the molecular mechanisms by which such extrachromosomal elements are generated and we traced the fate of these amplification intermediates over time. The model system consists of a Chinese hamster cell line (L46) created by gene transfer in which the initial amplification product was shown previously to be an unstable extrachromosomal element containing an inverted duplication spanning more than 160 kilobases (J. C. Ruiz and G. M. Wahl, Mol. Cell. Biol. 8:4302-4313, 1988). In this study, we show that these molecules were formed by a process involving chromosomal deletion. Fluorescence in situ hybridization was performed at multiple time points on cells with amplified sequences. These studies reveal that the extrachromosomal molecules rapidly integrate into chromosomes, often near or at telomeres, and once integrated, the amplified sequences are themselves unstable. These data provide a molecular and cytogenetic chronology for gene amplification in this model system; an early event involves deletion to generate extrachromosomal elements, and subsequent integration of these elements precipitates a cascade of chromosome instability.
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37
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Abstract
Acentric extrachromosomal elements, such as submicroscopic autonomously replicating circular molecules (episomes) and double minute chromosomes, are common early, and in some cases initial, intermediates of gene amplification in many drug-resistant and tumor cell lines. In order to gain a more complete understanding of the amplification process, we investigated the molecular mechanisms by which such extrachromosomal elements are generated and we traced the fate of these amplification intermediates over time. The model system consists of a Chinese hamster cell line (L46) created by gene transfer in which the initial amplification product was shown previously to be an unstable extrachromosomal element containing an inverted duplication spanning more than 160 kilobases (J. C. Ruiz and G. M. Wahl, Mol. Cell. Biol. 8:4302-4313, 1988). In this study, we show that these molecules were formed by a process involving chromosomal deletion. Fluorescence in situ hybridization was performed at multiple time points on cells with amplified sequences. These studies reveal that the extrachromosomal molecules rapidly integrate into chromosomes, often near or at telomeres, and once integrated, the amplified sequences are themselves unstable. These data provide a molecular and cytogenetic chronology for gene amplification in this model system; an early event involves deletion to generate extrachromosomal elements, and subsequent integration of these elements precipitates a cascade of chromosome instability.
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Affiliation(s)
- J C Ruiz
- Gene Expression Laboratory, Salk Institute, La Jolla, California 92037
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38
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Von Hoff DD, Forseth B, Clare CN, Hansen KL, VanDevanter D. Double minutes arise from circular extrachromosomal DNA intermediates which integrate into chromosomal sites in human HL-60 leukemia cells. J Clin Invest 1990; 85:1887-95. [PMID: 2189894 PMCID: PMC296655 DOI: 10.1172/jci114650] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Amplification of oncogenes has been found to be an important prognostic factor in behavior of patients' malignancies. In this study we have used new gel electrophoresis techniques to follow the location of amplified c-myc oncogene sequences in HL-60 promyelocytic leukemia cells. In passages 46-62 of the cells, the cells contain amplified c-myc sequences on submicroscopic circular extrachromosomal DNA (episomes). With increased passages in culture (passages 63-72) the cells lose the episome c-myc sequences with a shift of those sequences to double minutes. With additional passage in culture, the c-myc shifts from the double minutes to a chromosomal site der(5)t(5;17)(q11.2;q?11.2). Concomitant with the shift of the c-myc sequences into the chromosomal compartment is a phenotypic change of a shortened cell-doubling time. These studies provide the first molecular evidence of a progression from a submicroscopic location for amplified oncogene sequences to a chromosomal location for the amplified sequences. This molecularly documented model can now be used to test various strategies to prevent incorporation of extrachromosomally located oncogene sequences into chromosomal sites. Prevention of integration of the oncogene sequences into chromosomal sites could modulate progression of patients' tumors.
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Affiliation(s)
- D D Von Hoff
- Department of Medicine, University of Texas Health Science Center, San Antonio 78284-7884
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39
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40
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Game JC, Sitney KC, Cook VE, Mortimer RK. Use of a ring chromosome and pulsed-field gels to study interhomolog recombination, double-strand DNA breaks and sister-chromatid exchange in yeast. Genetics 1989; 123:695-713. [PMID: 2693206 PMCID: PMC1203882 DOI: 10.1093/genetics/123.4.695] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We describe a system that uses pulsed-field gels for the physical detection of recombinant DNA molecules, double-strand DNA breaks (DSB) and sister-chromatid exchange in the yeast Saccharomyces cerevisiae. The system makes use of a circular variant of chromosome III (Chr. III). Meiotic recombination between this ring chromosome and a linear homolog produces new molecules of sizes distinguishable on gels from either parental molecule. We demonstrate that these recombinant molecules are not present either in strains with two linear Chr. III molecules or in rad50 mutants, which are defective in meiotic recombination. In conjunction with the molecular endpoints, we present data on the timing of commitment to meiotic recombination scored genetically. We have used x-rays to linearize circular Chr. III, both to develop a sensitive method for measuring frequency of DSB and as a means of detecting double-sized circles originating in part from sister-chromatid exchange, which we find to be frequent during meiosis.
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Affiliation(s)
- J C Game
- Division of Cellular and Molecular Biology, Lawrence Berkeley Laboratory, Berkeley, California 94720
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41
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Jongsma AP, Duijndam WA, Borst P. DNA content and structure of (double) minutes of a methotrexate-resistant cell line. HISTOCHEMISTRY 1989; 93:87-92. [PMID: 2693417 DOI: 10.1007/bf00266852] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have determined the DNA content of intact double minutes (DMs) and of single minutes (SMs) by fluorometry of the individual chromatin bodies in metaphase spreads after staining with Feulgen-Schiff pararosaniline. We find that the intact DMs and SMs of the methotrexate-resistant mouse cell line 3T6R50 contain 4.4 megabase pairs (Mb) and 2.6 Mb DNA respectively, using the DNA content of E. coli (4.7 Mb) as a reference. As the pulsed field gradient gel electrophoresis experiments by van der Bliek et al. (1988) have indicated that the minutes of 3T6R50 cells contain a homogeneous population of 2.5 Mb DNA circles, we conclude that a SM contains one circular double strand DNA molecule of approximately 2.5 Mb, whereas DMs contain two.
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Affiliation(s)
- A P Jongsma
- Department of Molecular Biology, The Netherlands Cancer Institute, Amsterdam
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42
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Abstract
In Chlamydomonas reinhardtii, mutations on an unusual linkage group, the uni linkage group (ULG), affect structure and function of basal bodies. The ULG shows Mendelian segregation, but its genetic map is circular. Molecular cloning of fragments of the ULG was accomplished by taking advantage of restriction fragment length polymorphisms generated by crosses to Chlamydomonas smithii. These clones were used as probes to determine the size and form of the ULG chromosome; it is a 6-9 megabase linear molecule. Use of the probes for in situ DNA hybridization in cells localized the ULG chromosome to basal bodies.
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Affiliation(s)
- J L Hall
- Rockefeller University, New York 10021
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43
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Ellenberger TE, Beverley SM. Multiple Drug Resistance and Conservative Amplification of the H Region in Leishmania major. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)63816-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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44
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Abstract
Mobility of supercoiled (form I) and nicked circular (form II) plasmid DNAs was determined on two major forms of pulsed-field electrophoresis, CHEF and OFAGE. Plasmids with molecular lengths ranging from 2.30 to 17.8 kilobase pairs (kb) were used with Saccharomyces cerevisiae chromosomes as standards. Agarose gel concentrations were varied from 0.3 to 2.0 percent, with higher percentage gels resolving forms I and II of smaller plasmids. The pulsing range of 3.7 to 240 seconds resulted in quite variable Saccharomyces chromosomal mobilities on both 0.5 and 1.0 percent gels, while both form I and II of all plasmid DNAs showed relatively constant mobilities with some increase at the shortest pulse times. Using a 30 second pulse time and gel concentrations of at least 1.0 percent, the usual order of migration of plasmid forms for a 17.8 kb plasmid could be changed. We interpret this result as an increase in the relative mobility of form II in our pulsed-field gel conditions.
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Affiliation(s)
- J S Simske
- Department of Microbiology, University of Minnesota, Minneapolis 55455
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45
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Delidakis C, Swimmer C, Kafatos FC. Gene amplification: an example of genome rearrangement. Curr Opin Cell Biol 1989; 1:488-96. [PMID: 2697268 DOI: 10.1016/0955-0674(89)90010-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- C Delidakis
- Department of Biology, Yale University, New Haven, Connecticut
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46
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Autonomously replicating episomes contain mdr1 genes in a multidrug-resistant human cell line. Mol Cell Biol 1989. [PMID: 2648129 DOI: 10.1128/mcb.9.1.109] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gene amplification in human tumor cells is frequently mediated by extrachromosomal elements (e.g., double minute chromosomes [DMs]). Recent experiments have shown that DMs can be formed from smaller, submicroscopic circular precursors referred to as episomes (S. M. Carroll, M. L. DeRose, P. Gaudray, C. M. Moore, D. R. Needham-Vandevanter, D. D. Von Hoff and G. M. Wahl, Mol. Biol. 8:1525-1533, 1988). To investigate whether episomes are generally involved as intermediates in gene amplification, we determined whether they mediate the amplification of the mdr1 gene, which when overexpressed engenders cross resistance to multiple lipophilic drugs. A variety of methods including electrophoresis of undigested DNAs in high-voltage gradients, NotI digestion, and production of double-strand breaks by gamma irradiation were used to distinguish between mdr1 sequences amplified on submicroscopic circular molecules and those amplified within DMs or chromosomal DNA. The gamma-irradiation procedure provides a new method for detecting and determining the size of circular molecules from 50 kilobases (kb) to greater than 1,000 kb. These methods revealed that some of the amplified mdr1 genes in vinblastine-resistant KB-V1 cells are contained in supercoiled circular molecules of approximately 600 and approximately 750 kb. Analysis of the replication of these molecules by a Meselson-Stahl density shift experiment demonstrated that they replicate approximately once in a cell cycle. The data lend further support to a model for gene amplification in which DMs are generally formed from smaller, autonomously replicating precursors.
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47
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Chen TL, Manuelidis L. Neuroblastoma double minutes isolated by pulsed-field gel electrophoresis without prior strand-cleaving treatments. Genomics 1989; 4:430-3. [PMID: 2714799 DOI: 10.1016/0888-7543(89)90351-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In a human neuroblastoma line, minute chromosomes were separable from the bulk of interphase nuclear DNA by contour-clamped homogeneous electric field (CHEF) gel electrophoresis. The minute chromosomes showed a homogeneous size of approximately 3 Mbp and contained amplified N-myc genes. Fractionation was accomplished without prior strand-cleaving treatment of the DNA, indicating that at least a portion of the minute chromosomes exist as free entities in the interphase nuclei. Human alphoid satellite DNA sequences were also detected in the 3-Mbp band. It is possible that alphoid sequences are contained in the constricted central region that joins these double minutes.
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Affiliation(s)
- T L Chen
- Section of Neuropathology, Yale University School of Medicine, New Haven, Connecticut 06511
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48
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Beverley SM. Estimation of circular DNA size using gamma-irradiation and pulsed-field gel electrophoresis. Anal Biochem 1989; 177:110-4. [PMID: 2742141 DOI: 10.1016/0003-2697(89)90023-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A method is described for estimating the size of large circular DNAs found within complex chromosomal DNA preparations. DNAs are treated with low levels of gamma-irradiation, sufficient to introduce a single double-stranded break per circle, and the resulting linear DNA is sized by pulsed-field electrophoresis and blot hybridization. The method is fast, reproducible, and very conveniently applied to the agarose-enclosed chromosomal DNA preparations commonly used in pulsed field electrophoresis.
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Affiliation(s)
- S M Beverley
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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49
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Ruiz JC, Choi KH, von Hoff DD, Roninson IB, Wahl GM. Autonomously replicating episomes contain mdr1 genes in a multidrug-resistant human cell line. Mol Cell Biol 1989; 9:109-15. [PMID: 2648129 PMCID: PMC362151 DOI: 10.1128/mcb.9.1.109-115.1989] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Gene amplification in human tumor cells is frequently mediated by extrachromosomal elements (e.g., double minute chromosomes [DMs]). Recent experiments have shown that DMs can be formed from smaller, submicroscopic circular precursors referred to as episomes (S. M. Carroll, M. L. DeRose, P. Gaudray, C. M. Moore, D. R. Needham-Vandevanter, D. D. Von Hoff and G. M. Wahl, Mol. Biol. 8:1525-1533, 1988). To investigate whether episomes are generally involved as intermediates in gene amplification, we determined whether they mediate the amplification of the mdr1 gene, which when overexpressed engenders cross resistance to multiple lipophilic drugs. A variety of methods including electrophoresis of undigested DNAs in high-voltage gradients, NotI digestion, and production of double-strand breaks by gamma irradiation were used to distinguish between mdr1 sequences amplified on submicroscopic circular molecules and those amplified within DMs or chromosomal DNA. The gamma-irradiation procedure provides a new method for detecting and determining the size of circular molecules from 50 kilobases (kb) to greater than 1,000 kb. These methods revealed that some of the amplified mdr1 genes in vinblastine-resistant KB-V1 cells are contained in supercoiled circular molecules of approximately 600 and approximately 750 kb. Analysis of the replication of these molecules by a Meselson-Stahl density shift experiment demonstrated that they replicate approximately once in a cell cycle. The data lend further support to a model for gene amplification in which DMs are generally formed from smaller, autonomously replicating precursors.
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Affiliation(s)
- J C Ruiz
- Gene Expression Laboratory, Salk Institute, La Jolla, California 92037
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50
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White TC, Fase-Fowler F, van Luenen H, Calafat J, Borst P. The H circles of Leishmania tarentolae are a unique amplifiable system of oligomeric DNAs associated with drug resistance. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37486-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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