Histone Variants: Methods and Protocols

Preface...

Table of Contents...

Contributing Authors...

Part I Biochemistry

1. Methods for Preparing Nucleosomes Containing Histone Variants

Tomoya Kujirai, Yasuhiro Arimura, Risa Fujita, Naoki Horikoshi, Shinichi Machida, and Hitoshi Kurumizaka

2. Characterization of Post-Translational Modifications on Histone Variants

Francisco Saavedra, Sebastián Marty-Lombardi, and Alejandra Loyola

3. Purification of Histone Variant-Interacting Chaperone Complexes

Hideaki Tagami

4. Detection of Histone Modification Dynamics during the Cell Cycle by MS-Based Proteomics

Moritz Carl Völker-Albert, Andreas Schmidt, Teresa Barth, Ignasi Forne, and Axel Imhof

Part II Epigenomics

5. Histone Native Chromatin Immunprecipitation

Alicia Alonso, Emily Bernstein, and Dan Hasson

6. How to Tackle Challenging ChIP-seq, with Long-Range Cross-Linking, using ATRX as an Example

Julia Truch, Jelena Telenius, Douglas R. Higgs, and Richard J. Gibbons

7. Time-ChIP : A Method to Determine Long-Term Locus-Specific Nucleosome Inheritance

Wojciech Siwek, Mariluz Gómez-Rodríguez, Daniel Sobral, Ivan R. Corrêa, and Lars E.T. Jansen

8. MINCE-seq : Mapping In Vivo Nascent Chromatin with EdU and Sequencing

Srinivas Ramachandran and Steven Henikoff

9. RChIP-seq : Chromatin-Associated RNA Sequencing in Developmentally Staged Mouse Testes

Tatiana A. Soboleva and David J. Tremethick

Jakub Mieczkowski and Michael Y. Tolstorukov

Part III Microscopy and Cell Biology

11. Imaging newly Synthesized and Old Histone Variant Dynamics Dependent on Chaperones Using the SNAP-Tag System

Júlia Torné, Guillermo Orsi, Dominique Ray-Gallet, and Geneviève Almouzni

12. Real Time de novo Deposition of Centromeric Histone-Associated Proteins Using the Auxin Inducible Degradation System

Sebastian Hoffmann and Daniele Fachinetti

13. Live Imaging of Parental Histone Variant Dynamics in UVC-Damaged Chromatin

Juliette Dabin, Anna Fortuny, Sandra Piquet, and Sophie E. Polo

14. CRISPR/Cas9 Gene Editing of Human Histone H2A Variant H2AX and MacroH2A

Justin W.C. Leung, Lara E. Emery, and Kyle M. Miller

Part IV Evolution, Development, and Diseases

15. Studying the Evolution of Histone Variants Using Phylogeny

16. Characterization of Post-Meiotic Male Germ Cell Genome Organizational States

Jérôme Govin, Sophie Barral, Yuichi Morozumi, Naghmeh Hoghoughi, Thierry Buchou, Sophie Rousseaux, and Saadi Khochbin

17. An Animal Model for Genetic Analysis of Multi-Gene Families : Cloning and Transgenesis of Large Tandemly-Repeated Histone Gene Clusters

18. Imaging and Quantitation of Assembly Dynamics of the Centromeric Histone H3 Variant CENP-A in Drosophila melanogaster Spermatocytes by Immunofluorescence and Fluorescence In-Situ Hybridization (Immuno-FISH)

Caitríona M. Collins and Elaine M. Dunleavy