151
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Murray JI, Bao Z, Boyle TJ, Boeck ME, Mericle BL, Nicholas TJ, Zhao Z, Sandel MJ, Waterston RH. Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat Methods 2008; 5:703-9. [PMID: 18587405 DOI: 10.1038/nmeth.1228] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2008] [Accepted: 05/29/2008] [Indexed: 11/09/2022]
Abstract
We describe a system that permits the automated analysis of reporter gene expression in Caenorhabditis elegans with cellular resolution continuously during embryogenesis. We demonstrate its utility by defining the expression patterns of reporters for several embryonically expressed transcription factors. The invariant cell lineage permits the automated alignment of multiple expression profiles, allowing direct comparison of the expression of different genes' reporters. We also used this system to monitor perturbations to normal development involving changes both in cell-division timing and in cell fate. Systematic application of this system could reveal the gene activity of each cell throughout development.
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Affiliation(s)
- John Isaac Murray
- Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
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152
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153
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Poser I, Sarov M, Hutchins JRA, Hériché JK, Toyoda Y, Pozniakovsky A, Weigl D, Nitzsche A, Hegemann B, Bird AW, Pelletier L, Kittler R, Hua S, Naumann R, Augsburg M, Sykora MM, Hofemeister H, Zhang Y, Nasmyth K, White KP, Dietzel S, Mechtler K, Durbin R, Stewart AF, Peters JM, Buchholz F, Hyman AA. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods 2008; 5:409-15. [PMID: 18391959 PMCID: PMC2871289 DOI: 10.1038/nmeth.1199] [Citation(s) in RCA: 488] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Accepted: 03/17/2008] [Indexed: 12/11/2022]
Abstract
The interpretation of genome sequences requires reliable and standardized methods to assess protein function at high throughput. Here we describe a fast and reliable pipeline to study protein function in mammalian cells based on protein tagging in bacterial artificial chromosomes (BACs). The large size of the BAC transgenes ensures the presence of most, if not all, regulatory elements and results in expression that closely matches that of the endogenous gene. We show that BAC transgenes can be rapidly and reliably generated using 96-well-format recombineering. After stable transfection of these transgenes into human tissue culture cells or mouse embryonic stem cells, the localization, protein-protein and/or protein-DNA interactions of the tagged protein are studied using generic, tag-based assays. The same high-throughput approach will be generally applicable to other model systems.
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Affiliation(s)
- Ina Poser
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany
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154
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Lok JB, Artis D. Transgenesis and neuronal ablation in parasitic nematodes: revolutionary new tools to dissect host-parasite interactions. Parasite Immunol 2008; 30:203-14. [PMID: 18324923 DOI: 10.1111/j.1365-3024.2008.01006.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ease of experimental gene transfer into viral and prokaryotic pathogens has made transgenesis a powerful tool for investigating the interactions of these pathogens with the host immune system. Recent advances have made this approach feasible for more complex protozoan parasites. By contrast, the lack of a system for heritable transgenesis in parasitic nematodes has hampered progress toward understanding the development of nematode-specific cellular responses. Recently, however, significant strides towards such a system have been made in several parasitic nematodes, and the possible applications of these in immunological research should now be contemplated. In addition, methods for targeted cell ablation have been successfully adapted from Caenorhabditis elegans methodology and applied to studies of neurobiology and behaviour in Strongyloides stercoralis. Together, these new technical developments offer exciting new tools to interrogate multiple aspects of the host-parasite interaction following nematode infection.
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Affiliation(s)
- J B Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-6008, USA.
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155
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Bamps S, Hope IA. Large-scale gene expression pattern analysis, in situ, in Caenorhabditis elegans. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:175-83. [DOI: 10.1093/bfgp/eln013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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156
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Abstract
Drosophila melanogaster is a highly attractive model system for the study of numerous biological questions pertaining to development, genetics, cell biology, neuroscience and disease. Until recently, our ability to manipulate flies genetically relied heavily on the transposon-mediated integration of DNA into fly embryos. However, in recent years significant improvements have been made to the transgenic techniques available in this organism, particularly with respect to integrating DNA at specific sites in the genome. These new approaches will greatly facilitate the structure-function analyses of Drosophila genes, will enhance the ease and speed with which flies can be manipulated, and should advance our understanding of biological processes during normal development and disease.
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Affiliation(s)
- Koen J T Venken
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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157
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Abstract
Although substantial advances have been made in mycobacterial genetics over the past 15 yr, manipulation of mycobacterial genomes and Mycobacterium tuberculosis in particular, continues to be hindered by problems of relatively poor DNA uptake, slow growth rate, and high levels of illegitimate recombination. In Escherichia coli an effective approach to stimulating recombination frequencies has been developed called "recombineering," in which phage-encoded recombination functions are transiently expressed to promote efficient homologous recombination. Although homologs of these recombination proteins are rare among mycobacteriophages, we have identified one phage, Che9c, encoding relatives of both RecE and RecT of the E. coli rac prophage. Expression of the Che9c proteins from an inducible expression system in either slow- or fast-growing mycobacteria provides elevated recombination frequencies and facilitates simple allelic exchange using linear DNA substrates. Mycobacterial recombineering, therefore, offers a simple approach for constructing gene replacement mutants in M. smegmatis and M. tuberculosis.
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Affiliation(s)
- Julia C van Kessel
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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158
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Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastas D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, McKay S, Okada HM, Pan J, Schulz AK, Tu D, Wong K, Zhao Z, Alexeyenko A, Burglin T, Sonnhammer E, Schnabel R, Jones SJ, Marra MA, Baillie DL, Moerman DG. High-throughput in vivo analysis of gene expression in Caenorhabditis elegans. PLoS Biol 2007; 5:e237. [PMID: 17850180 PMCID: PMC1971126 DOI: 10.1371/journal.pbio.0050237] [Citation(s) in RCA: 289] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 07/05/2007] [Indexed: 11/18/2022] Open
Abstract
Using DNA sequences 5' to open reading frames, we have constructed green fluorescent protein (GFP) fusions and generated spatial and temporal tissue expression profiles for 1,886 specific genes in the nematode Caenorhabditis elegans. This effort encompasses about 10% of all genes identified in this organism. GFP-expressing wild-type animals were analyzed at each stage of development from embryo to adult. We have identified 5' DNA regions regulating expression at all developmental stages and in 38 different cell and tissue types in this organism. Among the regulatory regions identified are sequences that regulate expression in all cells, in specific tissues, in combinations of tissues, and in single cells. Most of the genes we have examined in C. elegans have human orthologs. All the images and expression pattern data generated by this project are available at WormAtlas (http://gfpweb.aecom.yu.edu/index) and through WormBase (http://www.wormbase.org).
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Affiliation(s)
- Rebecca Hunt-Newbury
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan Viveiros
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert Johnsen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Allan Mah
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Dina Anastas
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lily Fang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Erin Halfnight
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - John Lin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Adam Lorch
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sheldon McKay
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - H. Mark Okada
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Jie Pan
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ana K Schulz
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Domena Tu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kim Wong
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Z Zhao
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Andrey Alexeyenko
- Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Burglin
- Department of Biosciences, Karolinska Institutet, Huddinge, Sweden
| | - Eric Sonnhammer
- Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
| | - Ralf Schnabel
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Steven J Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - David L Baillie
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Donald G Moerman
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- * To whom correspondence should be addressed. E-mail:
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159
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Hillier LW, Miller RD, Baird SE, Chinwalla A, Fulton LA, Koboldt DC, Waterston RH. Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny. PLoS Biol 2007; 5:e167. [PMID: 17608563 PMCID: PMC1914384 DOI: 10.1371/journal.pbio.0050167] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 04/17/2007] [Indexed: 12/18/2022] Open
Abstract
To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism-based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80-110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently.
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Affiliation(s)
- LaDeana W Hillier
- Genome Sequencing Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Raymond D Miller
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Scott E Baird
- Department of Biological Sciences, Wright State University, Dayton, Ohio, United States of America
| | - Asif Chinwalla
- Genome Sequencing Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Lucinda A Fulton
- Genome Sequencing Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Daniel C Koboldt
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Robert H Waterston
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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160
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Chan W, Costantino N, Li R, Lee SC, Su Q, Melvin D, Court DL, Liu P. A recombineering based approach for high-throughput conditional knockout targeting vector construction. Nucleic Acids Res 2007; 35:e64. [PMID: 17426124 PMCID: PMC1885671 DOI: 10.1093/nar/gkm163] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Revised: 03/05/2007] [Accepted: 03/05/2007] [Indexed: 12/30/2022] Open
Abstract
Functional analysis of mammalian genes in vivo is primarily achieved through analysing knockout mice. Now that the sequencing of several mammalian genomes has been completed, understanding functions of all the genes represents the next major challenge in the post-genome era. Generation of knockout mutant mice has currently been achieved by many research groups but only by making individual knockouts, one by one. New technological advances and the refinements of existing technologies are critical for genome-wide targeted mutagenesis in the mouse. We describe here new recombineering reagents and protocols that enable recombineering to be carried out in a 96-well format. Consequently, we are able to construct 96 conditional knockout targeting vectors simultaneously. Our new recombineering system makes it a reality to generate large numbers of precisely engineered DNA constructs for functional genomics studies.
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Affiliation(s)
- Waiin Chan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Nina Costantino
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Ruixue Li
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Song Choon Lee
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Qin Su
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - David Melvin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Donald L. Court
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
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161
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