Description
Hox Genes: Methods and Protocols explores techniques and methodologies which arose from or were successfully applied to the study of Hox genes and Hox proteins, at the intersection of experimental embryology, genetics, biochemistry, physiology, evolutionary biology and other life sciences. This detailed volume begins with a section on discovery and functional analysis of Hox genes and then it continues onward to discuss mode of action and biomedical applications of Hox proteins. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls. Expert and practical, Hox Genes: Methods and Protocols serves as an ideal guide to researchers striving to move forward in this dynamic and exciting area of study. Part I: Hox Genes: From Discovery to Functional Analysis 1. Discovery and Classification of Homeobox Genes in Animal Genomes Ferdinand Marltaz, Jordi Paps, Ignacio Maeso, and Peter W.H. Holland 2. How to Study Hox Gene Expression and Function in Mammalian Oocytes and Early Embryos Delphine Paul, Caroline Sauvegarde, Ren Rezsohazy, and Isabelle Donnay 3. Genetic Lineage Tracing Analysis of Anterior Hox Expressing Cells Brigitte Laforest, Nicolas Bertrand, and Stphane Zaffran 4. A Genetic Strategy to Obtain P-Gal4 Elements in the Drosophila Hox Genes Luis de Navas, David Foronda, Delia del Saz, and Ernesto Snchez-Herrero 5. Hox Complex Analysis Through BAC Recombineering Mark Parrish, Youngwook Ahn, Christof Nolte, Bony De Kumar, and Robb Krumlauf 6. The Genetics of Murine Hox Loci: Tamere, String, and Panthere to Engineer Chromosome Variants Patrick Tschopp and Denis Duboule 7. Topological Organization of Drosophila Hox Genes Using DNA Fluorescent In Situ Hybridization Frdric Bantignies and Giacomo Cavalli 8. Mining the Cis-Regulatory Elements of Hox Clusters Navneet Kaur Matharu and Rakesh K. Mishra 9. Functional Analysis of Hox Genes in Zebrafish Franck Ladam and Charles G. Sagerstrm 10. Transgenesis in Non-Model Organisms: The Case of Parhyale Zacharias Kontarakis and Anastasios Pavlopoulos 11. Tissue Specific RNA Isolation in Drosophila Embryos: A Strategy to Analyze Context Dependent Transcriptome Landscapes Using FACS Arnaud Defaye and Laurent Perrin 12. Hox Transcriptomics in Drosophila Embryos Maria Polychronidou and Ingrid Lohmann Part II: Hox Proteins: Mode of Action and Biomedical Applications 13. Measuring Hox-DNA Binding by Electrophoretic Mobility Shift Analysis Kelly Churion, Ying Liu, Hao-Ching Hsiao, Kathleen S. Matthews, and Sarah E. Bondos 14. Chromatin Immunoprecipitation and Chromatin Immunoprecipitation with Massively Parallel Sequencing on Mouse Embryonic Tissue Shilu Amin and Nicoletta Bobola 15. ChIP for Hox Proteins from Drosophila Imaginal Discs Pavan Agrawal and L.S. Shashidhara 16. SELEX-seq: A Method for Characterizing the Complete Repertoire of Binding Site Preferences for Transcription Factor Complexes Todd R. Riley, Matthew Slattery, Namiko Abe, Chaitanya Rastogi, Richard Mann, and Harmen Bussemaker 17. DamID as an Approach to Studying Long Distance Chromatin Interactions Fabienne Clard, Franois Karch, and Robert K. Maeda 18. cgChIP: A Cell Type and Gene Specific Method for Chromatin Analysis Marios Agelopoulos, Daniel J. McKay, and Richard S. Mann 19. Bimolecular Fluorescence Complementation (BiFC) in Live Drosophila Embryos Marilyne Duffraisse, Bruno Hudry, and Samir Merabet 20. Hox Protein Interactions: Screening and Network Building Isabelle Bergiers, Barbara Lambert, Sarah Daakour, Jean-Claude Twizere, and Ren Rezsohazy 21. Rational Drug Repurposing Using sscMap Analysis in a HOX-TALE Model of Leukemia Laura M.J. Kettyle, Fabio G. Liberante, and Alexander Thompson
