Strategies for studying gene regulation mechanisms have changed dramatically over the

Transcription

1 By Michael F. Carey, University of California, Los Angeles; Craig L. Peterson, University of Massachusetts Medical School, Worcester; and Stephen T. Smale, University of California, Los Angeles Strategies for studying gene regulation mechanisms have changed dramatically over the past several years in light of the emergence of complete genome sequences for many organisms as well as the development of or improvements to technologies such as chromatin immunoprecipitation, RNA interference, microarrays, and proteomics. The first edition of the highly successful Transcriptional Regulation in Eukaryotes, written by Michael Carey and Stephen Smale at UCLA, provided a comprehensive source of strategic, conceptual, and technical information for investigating the complexities of gene regulation at the level of transcription. With the ever-increasing importance of genome data and the appearance of new and better techniques, the second edition of this book has added a third author, Craig Peterson at the University of Massachusetts Medical School. In addition to a new chapter on the in vitro analysis of chromatin templates for DNA-binding studies and transcription, this second edition has been extensively rewritten and updated to discuss new advances in the field and their impact on gene regulation mechanisms. The second edition retains the approach of the first in covering both the conceptual and practical aspects of how to study the regulation of a newly isolated gene and the biochemistry of a new transcription factor. Transcriptional Regulation in Eukaryotes serves as both a powerful textbook and manual for advanced instruction in molecular biology which supplements clearly written text with extensive illustrations puts methods in the context of underlying theory gives expert recommendations on experimental strategies encourages creativity in investigative design explains protocols for essential techniques step by step, with extensive advice on troubleshooting provides the latest methods in use in the field This important and unique book is essential reading for anyone pursuing the analysis of gene expression in model systems or disease states, providing underlying theory and perspective to the newcomer and the latest techniques to the expert. Published in December 2008, 620 pp., appendix, index Hardcover $240 ISBN Paperback $165 ISBN CONTENTS Preface Overview Abbreviations and Acronyms 1. A Primer on Transcriptional Regulation in Mammalian Cells 2. Initial Strategic Issues 3. Transcription Initiation Site Mapping 4. Functional Assays for Promoter Analysis 5. Identification and Analysis of Distant Control Regions 6. Identifying cis-acting DNA Elements within a Control Region 7. Identification of DNA-Binding Proteins and Their Genes 8. Confirming the Functional Importance of a Protein DNA Interaction 9. In Vivo Analysis of an Endogenous Control Region 10. Identifying and Characterizing Domains of Transcription Regulatory Factors 11. DNA Binding by Regulatory Transcription Factors 12. Transcription and Preinitiation Complex Assembly In Vitro 13. Studying Chromatin Dynamics In Vitro: Chromatin Assembly, Remodeling, and Transcription Appendix: Cautions Index To order or request additional information, please visit our website or: Call: (Continental US and Canada) (All other locations) Fax: cshpress@cshl.edu Write: Cold Spring Harbor Laboratory Press, 500 Sunnyside Blvd., Woodbury, NY

2 By Andrew J. Link, Vanderbilt University School of Medicine, Nashville, Tennessee and Joshua LaBaer, Harvard University School of Medicine Based on a popular course at Cold Spring Harbor Laboratory, this new manual assembles cutting edge protocols, helpful hints, and lecture notes to teach researchers from a wide variety of disciplines the essential methods of proteomics using state of the art instrumentation. Detailed protocols involving protein microarrays, liquid chromatography, high throughput cloning of expression constructs, IMAC, mass spectrometry, MALDI TOF, and MudPIT are provided, along with well illustrated descriptions of experimental procedures and lists of recommended Web sites and reading material. Proteomics: A Cold Spring Harbor Laboratory Course Manual can be used both as the basis for a course and as a detailed bench manual for those performing indispensable proteomic experiments. It is authored by Andrew J. Link and Joshua LaBaer, both leaders in their fields, who bring complementary expertise to the manual. Published in December 2008, 232 pp., illus., appendices, index Hardcover $150 ISBN Paperback $94 ISBN CONTENTS Preface Introduction Experiments 1. Analysis of Whole-cell Lysates by Twodimensional Gel Electrophoresis and MALDI Mass Spectrometry 2. Purification of Protein Complexes for Mass Spectrometry Analysis 3. Qualitative and Quantitative Measurement of Peptides with MALDI TOF/TOF Mass Spectrometry 4. Analysis of Protein Complexes: High-sensitivity Liquid Chromatography Coupled with Tandem Mass Spectrometry 5. Phosphopeptide Analysis Using IMAC and Mass Spectrometry 6. Multidimensional Protein Identification Technology (MudPIT) Analysis of Whole-cell Lysates 7. Quantitative Mass Spectrometry Analysis of Whole-cell Extracts (itraq) 8. Analysis and Validation of Tandem Mass Spectra 9. High-throughput Cloning of ORFs: Assembling Large Sets of Expression Constructs 10. Construction of Protein Microarrays Nucleic Acid Programmable Protein Array (NAPPA) 11. Using the Nucleic Acid Programmable Protein Array (NAPPA) for Identifying Protein Protein Interactions Appendices 1. Setup and Demonstration of a Nanoelectrospray Ionization (nanoesi) Source and Tandem Mass Spectrometry (MS/MS) 2. Solution Protein Digest 3. In-gel Trypsin Digest of Gel Fractionated Proteins 4. Trichloroacetic Acid (TCA) Precipitation of Proteins 5. Monoisotopic and Immonium Ion Masses of Amino Acids 6. Dipeptide Masses of Amino Acids 7. LTQ Instrument Methods 8. Off-line Desalting of Peptide Mixtures 9. Preparing Competent Cells 10. DNA Quantification 11. Cautions Index To order or request additional information, please visit our website or: Call: (Continental US and Canada) (All other locations) Fax: cshpress@cshl.edu Write: Cold Spring Harbor Laboratory Press, 500 Sunnyside Blvd., Woodbury, NY

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6 The online source of trusted techniques in molecular and cell biology Contains cutting-edge and classic protocols presented step-by-step with cautions and troubleshooting Frequently updated and annotated Interactive, customizable, and fully searchable Subject Coverage Antibodies Bioinformatics/Genomics Cell Biology Chromatography Computational Biology DNA Delivery/Gene Transfer Electrophoresis Emerging Model Organisms Genetics High-Throughput Analysis Imaging/Microscopy Immunology Laboratory Organisms Molecular Biology Neuroscience Newly Added Protocols Plant Biology Polymerase Chain Reaction (PCR) Proteins and Proteomics RNA Interference (RNAi)/siRNA Stem Cells Transgenic Technology Cold Spring Harbor Laboratory is renowned for its teaching of biomedical research techniques. For decades, participants in its celebrated, hands-on courses and users of its laboratory manuals have gained access to the most authoritative and reliable methods in molecular and cellular biology. Now that access has moved online. Visit Cold Spring Harbor Protocols today and discover a rich, interactive source of new and classic research techniques. The site is fully searchable, with many tools that can be customized by users, including topic-based alerting and personal folders. Through a web-based editorial process, users also have the opportunity to add refereed comments to each protocol. Links in the online protocols offer additional resources and step-bystep instructions print out in a convenient form, complete with materials, cautions, and troubleshooting advice. Each protocol is citable, presented, and edited in the style that has made Molecular Cloning, Antibodies, Cells, and many other Cold Spring Harbor manuals essential to the work of scientists worldwide. The current collection of more than 1000 protocols is continuously expanded, updated, and annotated by the originators and users of the techniques. NEW to CSH Protocols: Emerging Model Organisms, a full-fledged guide to the use of new model systems in the laboratory, covering husbandry, genetics, genomics and basic protocols. CSH Protocols is created by Cold Spring Harbor Laboratory Press in association with HighWire Press of Stanford University. Executive Editor: Dr. David Crotty ISSN / online, monthly Available exclusively via institutional site license For pricing information or to request a free trial, contact us at: Phone: (Continental US and Canada) or (all other locations) Fax: cshpress@cshl.edu Website: Write: Cold Spring Harbor Laboratory Press, 500 Sunnyside Blvd., Woodbury, NY

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