Epigenome Editing: Methods and Protocols

ISBN-13: 9781493992812 / Angielski / Miękka / 2019 / 482 str.

Albert Jeltsch;Marianne G. Rots

Opis

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.

Spis treści

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 Büning

 

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 Pflüger, 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-François Deleuze, Florence Mauger, and Jörg Tost

 

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

            Elsa Leitão, 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

            Désirée Goubert, Mihály 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