Main description:

This detailed book explores the concepts and applications of epigenome editing, as presented by leading scientists in the field. Beginning with some general and topical reviews, the collection continues by covering the design of DNA-binding devices, optimization of the effector domains, readout of epigenome marks, and approaches for delivery at the cellular and organismal level. Written for the highly successful Methods in Molecular Biology series, 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 practical, Epigenome Editing: Methods and Protocols will be of great assistance to people new to the field but also to those already engaged, as epigenetic editing is still a relatively unexplored field with many issues to be resolved.

Contents:

Part I: General Reviews

1. Editing the Epigenome: Overview, Open Questions, and Directions of Future Development

Marianne G. Rots and Albert Jeltsch

2. Zinc Fingers, TALEs and CRISPR Systems: A Comparison of Tools for Epigenome Editing

Charlene Babra Waryah, Colette Moses, Mahira Arooj, and Pilar Blancafort

3. Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities

Dilara Sen and Albert J. Keung

4. Generation of TALE-Based Designer Epigenome Modifiers

Sandra Nitsch and Claudio Mussolino

Part II: Topical Reviews

5. Neuroepigenetic Editing

Peter J. Hamilton, Carissa J. Lim, Eric J. Nestler, and Elizabeth A. Heller

6. Allele-Specific Epigenome Editing

Pavel Bashtrykov and Albert Jeltsch

7. Key to Delivery: The (Epi-)Genome Editing Vector Toolbox

Sabrina Just and Hildegard Buning

8. CRISPR/dCas9 Switch Systems for Temporal Transcriptional Control

Rutger A.F. Gjaltema and Edda G. Schulz

Part III: Delivery Protocols

9. Delivery of Designer Epigenome Modifiers into Primary Human T Cells

Tafadzwa Mlambo, Marianna Romito, Tatjana I. Cornu, and Claudio Mussolino

10. Viral Expression of Epigenome Editing Tools in Rodent Brain Using Stereotaxic Surgery Techniques

Peter J. Hamilton, Carissa J. Lim, Eric J. Nestler, and Elizabeth A. Heller

11. Stable Expression of Epigenome Editors Via Viral Delivery and Genomic Integration

Carolin Kroll and Philipp Rathert

12. Purified-Protein Delivery to Activate an Epigenetically-Silenced Allele in Mouse Brain

Benjamin Pyles, Barbara J. Bailus, Henriette O'Geen, and David J. Segal

13. Non-Viral Methodology for Efficient Co-Transfection

Jessica A. Kretzmann, Cameron W. Evans, Marck Norret, Pilar Blancafort, and K. Swaminathan Iyer

Part IV: Histone Editing Readout Protocols

14. Chromatin Immunoprecipitation in Human and Yeast Cells

Jessica B. Lee and Albert J. Keung

15. Chromatin Immunoprecipitation and High Throughput Sequencing (ChIP-Seq): Tips and Tricks Regarding the Laboratory Protocol and Initial Downstream Data Analysis

Darren K. Patten, Giacomo Corleone, and Luca Magnani

Part V: DNA Methylation Editing Readout Protocols

16. Generation of Whole Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis

Dulce B. Vargas-Landin, Jahnvi Pfluger, and Ryan Lister

17. Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data

Tim Stuart, Sam Buckberry, and Ryan Lister

18. Whole Genome Bisulfite Sequencing for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution

Magali Kernaleguen, Christian Daviaud, Yimin Shen, Eric Bonnet, Victor Renault, Jean-Francois Deleuze, Florence Mauger, and Joerg Tost

19. Locus-Specific DNA Methylation Analysis by Targeted Deep Bisulfite Sequencing

Elsa Leitao, Jasmin Beygo, Michael Zeschnigk, Ludger Klein-Hitpass, Marcel Bargull, Sven Rahmann, and Bernhard Horsthemke

20. DNA Methylation Analysis by Bisulfite Conversion Coupled to Double Multiplexed Amplicon-Based Next-Generation Sequencing (NGS)

Pavel Bashtrykov and Albert Jeltsch

Part VI: Gene Expression Readout Protocols

21. Cell-to-Cell Transcription Variability as Measured by Single Molecule RNA FISH to Detect Epigenetic State Switching

William Beckman, Ilona M. Vuist, Hermannus Kempe, and Pernette J. Verschure

22. Establishment of Cell Lines Stably Expressing dCas-Fusions to Address Kinetics of Epigenetic Editing

Desiree Goubert, Mihaly Koncz, Antal Kiss, and Marianne G. Rots

Part VII: Special Application Protocols

23. Editing of DNA Methylation Using dCas9-Peptide Repeat and scFv-TET1 Catalytic Domain Fusions

Sumiyo Morita, Takuro Horii, and Izuho Hatada

24. Chemical Inducible dCas9-Guided Editing of H3K27 Acetylation in Mammalian Cells

Dan Gao and Fu-Sen Liang

25. Screening Regulatory Element Function with CRISPR/Cas9-Based Epigenome Editing

Tyler S. Klann, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach