Part I: Hox Genes: From Discovery to Functional Analysis
1. Discovery and Classification of Homeobox Genes in Animal Genomes
Ferdinand Marlétaz, 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, René Rezsohazy, and Isabelle Donnay
3. Genetic Lineage Tracing Analysis of Anterior Hox Expressing Cells
Brigitte Laforest, Nicolas Bertrand, and Stéphane 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 Sánchez-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
Frédéric 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. Sagerström
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 Cléard, François 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 René 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
