Epigenetic Reprogramming During Mouse Embryogenesis Methods and Protocols

This volume explores the latest techniques used to study and understand chromatin reprogramming in embryos and germ cells. Various culture systems are presented, which consist of invaluable tools to investigate many developmental processes. This book also looks at methods for direct examination of DNA, RNA, and proteins in embryos, along with low-input and single-cell assays for exploring these features at the genome-wide scale. 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.

Cutting-edge and thorough, Epigenetics Reprogramming During Mouse Embryogenesis: Methods and Protocols is a valuable resource for any scientist and researcher looking to make new discoveries in this fascinating field of chromatin reprogramming. 

Preface…
Table of Contents…
Contributing Authors…

1. Ex Vivo Culture for Preimplantation Mouse Embryo to Analyse Pluripotency
Katia Boutourlinsky, Nicolas Allègre, and Claire Chazaud

2. Microfabricated Device for High Resolution Imaging of Preimplantation Embryos
Sandrine Vandormael-Pournin, Emmanuel Frachon, Samy Gobaa, and Michel Cohen-Tannoudji

3. In Vitro Culture of Mouse Blastocyst to the Egg Cylinder Stage via Mural Trophectoderm Excision
Hatice O. Ozguldez and Ivan Bedzhov

4. Spatially Organized Differentiation of Mouse Pluripotent Stem Cells on Micropatterned Surfaces
Sophie M. Morgani and Anna-Katerina Hadjantonakis 

5. Mouse Primordial Germ Cells: In Vitro Culture and Conversion to Pluripotent Stem Cell Lines
Malgorzata Borkowska and Harry G. Leitch

6. Generation of Primordial Germ Cell-Like Cells in Small and Large Scales
Wolfram H. Gruhn and Ufuk Günesdogan

7. Genome-Scale CRISPR Screening for Regulators of Cell Fate Transitions
Valentina Carlini, Kristjan H. Gretarsson, and Jamie A. Hackett

8. Somatic Reprogramming by Nuclear Transfer 
Vincent Brochard and Nathalie Beaujean

9. Targeted Transgenic Mice using CRISPR/Cas9 Technology
Fatima El Marjou, Colin Jouhanneau, and Denis Krndija

10. Whole-Mount Immunofluorescence Staining of Early Mouse Embryos
Frederick C. K. Wong  

11. Investigating the Inner Cell Mass of the Mouse Blastocyst by Combined Immunofluorescence Staining and RNA Fluorescent In Situ Hybridization
Maud Borensztein 

12. Mapping of Chromosome Territories by 3D-Chromosome Painting during Early Mouse Development
Katia Ancelin, Yusuke Miyanari, Olivier Leroy, Maria-Elena Torres-Padilla, and Edith Heard

13. Deciphering the Early Mouse Embryo Transcriptome by Low-Input RNA-seq
Raquel Pérez-Palacios, Patricia Fauque, Aurélie Teissandier, and Déborah Bourc’his

14. Studying DNA Methylation Genome-Wide by Bisulfite Sequencing from Low Amounts of DNA in Mammals
Ambre Bender, Hala Al Adhami, Thomas Dahlet, and Michael Weber

15. Profiling DNA Methylation Genome-Wide in Single Cells
Antonio Galvao and Gavin Kelsey 

16. Tracking Histone Modifications in Embryos and Low Input Samples using Ultrasensitive STAR ChIP-seq
Bingjie Zhang, Xu Peng, Feng Xu, and Wei Xie

17. Chromatin Profiling in Mouse Embryonic Germ Cells by CUT&RUN
Srinivasa Abishek Prakash and Joan Barau 

18. DamID to Map Genome-Protein Interactions in Pre-Implantation Mouse Embryos
Mrinmoy Pal, Kim de Luca, Jop Kind, and Maria-Elena Torres-Padilla

19. Understanding Chromosome Structure during Early Mouse Development by Single-Cell Hi-C Analysis
Noémie Ranisavljevic, Maud Borensztein, and Katia Ancelin 

20. Bioinformatic Analysis of Single Cell Hi-C Data from Early Mouse Embryo
Samuel Collombet, Yuvia A. Pérez-Rico, Katia Ancelin, Nicolas Servant, and Edith Heard 

Subject Index List...