X-Chromosome Inactivation Methods and Protocols

This book details recently developed technologies and conventionally employed cytological proceduresfor the study of X-Chromosome Inactivation. Chapters detail live imaging, bioinformatic methods, fluorescence in situ hybridization, and immunofluorescence, and procedures to optimize the study of molecular mechanism underlying X chromosome inactivation. 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.

Authoritative and cutting-edge, X-Chromosome Inactivation: Methods Protocols aims to be useful for researchers in the field of epigenetics, chromatin, noncoding RNA, and nuclear architecture.

1. Screening for Factors Involved in X Chromosome Inactivation using Haploid ESCs

Asun Monfort, Giulio Di Minin, and Anton Wutz

2. Unbiased Genetic Screen to Identify Factors Involved in X-chromosome Inactivation Using a Pooled Bar-coded shRNA Library

Benoit Moindrot and Neil Brockdorff

3. Unbiased Genetic Screen to Identify Factors Involved in X-chromosome Inactivation Using a Pooled Bar-coded shRNA Library

Benoit Moindrot and Neil Brockdorff

4. Manipulation of Xist Imprinting in Mouse Pre-implantation Embryos

Atsushi Fukuda, Akihiro Umezawa, and Hidenori Akutsu

5. Somatic Cell Nuclear Transfer in Mice — Basic Protocol and Its Modification for Correcting X Chromosome Inactivation Status

Kimiko Inoue, Shogo Matoba, and Atsuo Ogura

Osamu Masui, Edith Heard, and Haruhiko Koseki

7. Live Imaging of X-chromosome Inactivation and Reactivation Kinetics

Shin Kobayashi

8. Visualizing the Dynamics of Inactive X chromosomes in Living Cells Using Antibody-based Fluorescent Probes

Yuko Sato, Timothy J Stasevich, and Hiroshi Kimura

9. Visualization of Hidden Epitopes at the Inactive X Chromosome

Emma R Stewart and Dawn Coverley

Kris G. Alavattam, Hironori Abe, Akihiko Sakashita, and Satoshi H. Namekawa

11. Simultaneous RNA-DNA FISH in Mouse Pre-implantation Embryos

Aristea Magaraki, Agnese Loda, Joost Gribnau, and Willy M. Baarends

12. Combined Immunofluorescence, RNA FISH and DNA FISH in Pre-implantation Mouse Embryos

Ikuhiro Okamoto

13. RNA-FISH and Immunofluorescence of Mouse Pre- and Post-implantation Embryos

Hirosuke Shiura, Yuka Sakata, Kuniya Abe, and Takashi Sado

14. Experimental Analysis of Imprinted Mouse X-chromosome Inactivation

Marissa Cloutier, Clair Harris, Srimonta Gayen, Emily Maclary, and

Sundeep Kalantry

15. X-chromosome Inactivation and Escape from X inactivation in Mouse

Wenxiu Ma, Giancarlo Bonora, Joel B Berletch, Xinxian Deng, William S. Noble, and Christine M. Disteche

16. Practical Analysis of Hi-C Data: Generating A/B Compartment Profiles

Hisashi Miura, Rawin Poonperm, Saori Takahashi, and Ichiro Hiratani