- Email: [email protected]
Methods in cell cycle research
Methods 41 (2007) 141–142 www.elsevier.com/locate/ymeth
Introduction
Methods in cell cycle research
The study of the cell cycle impacts diverse areas of research encompassing cancer biology, development, and basic aspects of cell biology. Rapid advances in our understanding of cell cycle regulation have been made possible by the application and development of methodologies from distinct disciplines, ranging from biochemistry, through imaging, to genetics. An explosion in our knowledge was also facilitated by the recent application of high-throughput approaches. Although initially developed for simple model organisms such as yeast, these approaches can now be applied more broadly to other systems, including mammalian cells. In assembling this collection, we tried to provide a broad and accessible overview of selected topics in the cell cycle field. Our hope is that this collection will be helpful for novices in the cell cycle field as well as experts who wish to explore a different experimental system. Topics covered fall into three general categories: (1) methodologies related to cell cycle analyses, (2) the use of model organisms for cell cycle studies, and (3) the application of computational analyses to cell cycle processes. In the area of cell cycle analysis, we begin with a comprehensive discussion of the study of cell cycle progression in mammalian tissue culture cells. Schorl and Sedivy provide modern tools for addressing classical questions concerning the lengths of cell cycle phases and the timing of the restriction point. The remaining reviews in this section focus on specific cell cycle processes. Feng et al. describe an elegant new method for analyzing active origins of DNA replication in yeast, taking advantage of the powerful ‘‘ChIP-on-chip’’ technology (microarray analysis after chromatin immunoprecipitation). Mora-Bermu´dez and Ellenberg discuss the use of fluorescence microscopy to study chromosome compaction and dynamics in living cells. Motegi and Myung describe quantitative assays for gross chromosomal rearrangement in yeast. These assays can be used to study the effects DNA damage and repair pathways on chromosome instability, a major process in the development of human cancers. Gassmann et al. discuss how to study the multitude of kinetochore proteins and their functions, both in
1046-2023/$ - see front matter Ó 2006 Elsevier Inc. All rights reserved. doi:10.1016/j.ymeth.2006.07.021
human cells and in the model organism, Caenorhabditis elegans. Proper kinetochore function is key to the faithful transmission of chromosomes and provides the initiation site for signaling by the spindle assembly checkpoint. Over the years, model organisms have provided important insights into the process of cell cycle regulation. In the next group of reviews we wished to illustrate the strengths of several experimental systems that are based on model organisms. Golden and O’Connell describe the powerful approach of gene inactivation by RNAi in combination with live cell imaging in the worm Caenorhabditis elegans. Garcia et al. illustrate how the various types of cell cycles that occur during Drosophila development can be used to understand cell cycle regulation. The yeast Saccharomyces cerevisiae has long been the organism of choice for many cell cycle studies, and Pan et al. describe a high-throughput method for analyzing genome-wide genetic interactions. Finally, Lupardus et al. provide a useful guide to cell cycle studies using a variety of Xenopus egg extracts. Taken together, these reviews encompass a wide range of methodologies that utilize diverse experimental approaches, including genetics, cytology, and biochemistry. Quantitative approaches have become increasingly important to biology in general and to the rapidly developing field of systems biology. We end our collection with two reviews that describe different approaches to modeling aspects of the cell cycle. Gardner et al. discuss the integration of computational modeling and quantitative digital fluorescence microscopy, moving back and forth between theory and experiment so that modeling can help design experiments and so that experimental findings lead to refinements in the models. Finally, Sible and Tyson describe the mathematical modeling of the cell cycle engine, with particular emphasis on the early frog cell cycle. They provide a discussion of the approach and links to software that will be helpful to the beginner and the expert alike. Several compilations published in recent years have addressed cell-cycle-related methodologies not emphasized in
142
Editorial / Methods 41 (2007) 141–142
this issue. In particular, we would like to point out a recent issue of Methods titled ‘‘New Approaches to Research on Mitosis’’ (Volume 38, No. 1, January 2006). For comprehensive reviews of methods relating to ubiquitin-mediated proteolysis and the cell cycle, see ‘‘Ubiquitin and Protein Degradation,’’ Parts A and B, Methods in Enzymology, Volumes 398 and 399. We hope that readers will find this collection both enlightening and useful.
Mark Solomon Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, CT 06520, USA E-mail address: [email protected] Orna Cohen-Fix * The Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, MD 20892, USA E-mail addresses: [email protected] Accepted 11 July 2006
*
Corresponding author.
Introduction
Methods in cell cycle research
The study of the cell cycle impacts diverse areas of research encompassing cancer biology, development, and basic aspects of cell biology. Rapid advances in our understanding of cell cycle regulation have been made possible by the application and development of methodologies from distinct disciplines, ranging from biochemistry, through imaging, to genetics. An explosion in our knowledge was also facilitated by the recent application of high-throughput approaches. Although initially developed for simple model organisms such as yeast, these approaches can now be applied more broadly to other systems, including mammalian cells. In assembling this collection, we tried to provide a broad and accessible overview of selected topics in the cell cycle field. Our hope is that this collection will be helpful for novices in the cell cycle field as well as experts who wish to explore a different experimental system. Topics covered fall into three general categories: (1) methodologies related to cell cycle analyses, (2) the use of model organisms for cell cycle studies, and (3) the application of computational analyses to cell cycle processes. In the area of cell cycle analysis, we begin with a comprehensive discussion of the study of cell cycle progression in mammalian tissue culture cells. Schorl and Sedivy provide modern tools for addressing classical questions concerning the lengths of cell cycle phases and the timing of the restriction point. The remaining reviews in this section focus on specific cell cycle processes. Feng et al. describe an elegant new method for analyzing active origins of DNA replication in yeast, taking advantage of the powerful ‘‘ChIP-on-chip’’ technology (microarray analysis after chromatin immunoprecipitation). Mora-Bermu´dez and Ellenberg discuss the use of fluorescence microscopy to study chromosome compaction and dynamics in living cells. Motegi and Myung describe quantitative assays for gross chromosomal rearrangement in yeast. These assays can be used to study the effects DNA damage and repair pathways on chromosome instability, a major process in the development of human cancers. Gassmann et al. discuss how to study the multitude of kinetochore proteins and their functions, both in
1046-2023/$ - see front matter Ó 2006 Elsevier Inc. All rights reserved. doi:10.1016/j.ymeth.2006.07.021
human cells and in the model organism, Caenorhabditis elegans. Proper kinetochore function is key to the faithful transmission of chromosomes and provides the initiation site for signaling by the spindle assembly checkpoint. Over the years, model organisms have provided important insights into the process of cell cycle regulation. In the next group of reviews we wished to illustrate the strengths of several experimental systems that are based on model organisms. Golden and O’Connell describe the powerful approach of gene inactivation by RNAi in combination with live cell imaging in the worm Caenorhabditis elegans. Garcia et al. illustrate how the various types of cell cycles that occur during Drosophila development can be used to understand cell cycle regulation. The yeast Saccharomyces cerevisiae has long been the organism of choice for many cell cycle studies, and Pan et al. describe a high-throughput method for analyzing genome-wide genetic interactions. Finally, Lupardus et al. provide a useful guide to cell cycle studies using a variety of Xenopus egg extracts. Taken together, these reviews encompass a wide range of methodologies that utilize diverse experimental approaches, including genetics, cytology, and biochemistry. Quantitative approaches have become increasingly important to biology in general and to the rapidly developing field of systems biology. We end our collection with two reviews that describe different approaches to modeling aspects of the cell cycle. Gardner et al. discuss the integration of computational modeling and quantitative digital fluorescence microscopy, moving back and forth between theory and experiment so that modeling can help design experiments and so that experimental findings lead to refinements in the models. Finally, Sible and Tyson describe the mathematical modeling of the cell cycle engine, with particular emphasis on the early frog cell cycle. They provide a discussion of the approach and links to software that will be helpful to the beginner and the expert alike. Several compilations published in recent years have addressed cell-cycle-related methodologies not emphasized in
142
Editorial / Methods 41 (2007) 141–142
this issue. In particular, we would like to point out a recent issue of Methods titled ‘‘New Approaches to Research on Mitosis’’ (Volume 38, No. 1, January 2006). For comprehensive reviews of methods relating to ubiquitin-mediated proteolysis and the cell cycle, see ‘‘Ubiquitin and Protein Degradation,’’ Parts A and B, Methods in Enzymology, Volumes 398 and 399. We hope that readers will find this collection both enlightening and useful.
Mark Solomon Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, CT 06520, USA E-mail address: [email protected] Orna Cohen-Fix * The Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, MD 20892, USA E-mail addresses: [email protected] Accepted 11 July 2006
*
Corresponding author.