Epigenomics: Methods and Protocols

ISBN-13: 9781071627235 / Angielski / Twarda / 2022

Hatada, Izuho

Opis

This detailed volume provides a comprehensive collection of protocols for epigenomic research, powering our ability to analyze epigenetic modifications across the entire genome. Beginning with methods used to investigate epigenomic modifications such as DNA methylation, histone modifications, and chromatin structure, the book continues with methods for manipulating the epigenome, including platforms for epigenome editing, inducible systems for epigenome editing, and epigenetically modified animals. Written for the highly successful Methods in Molecular Biology series, chapters feature introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Epigenomics: Methods and Protocols serves as an ideal resource for researchers looking to further expand the utility and scope of epigenomics research.

Spis treści

Part I: Analysis of the Epigenome: DNA Methylation

 

1. DNA Methylation Analysis Using Bisulfite Pyrosequencing

            Ken Higashimoto, Satoshi Hara, and Hidenobu Soejima

 

2. Post-Bisulfite Adaptor Tagging Based on an ssDNA Ligation Technique (tPBAT)

            Fumihito Miura, Yukiko Shibata, Miki Miura, and Takashi Ito

 

3. Reduced Representation Bisulfite Sequencing (RRBS)

            Kazuhiko Nakabayashi, Michihiro Yamamura, Keita Haseagawa, and Kenichiro Hata

 

Part II: Analysis of the Epigenome: Histone Modification and Chromatin Structure

 

4. Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers

            Shinjiro Hino, Tetsuya Sato, and Mitsuyoshi Nakao

 

5. ATAC-Seq Analysis of Accessible Chromatin: From Experimental Steps to Data Analysis

            Mayu Tatara, Taiyo Ikeda, Satoshi H. Namekawa, and So Maezawa

 

6. Low-Input CUT&RUN for Mouse Oocytes and Preimplantation Embryos

            Ryoya Hayashi and Azusa Inoue

 

7. Imaging Chromatin Accessibility by Assay of Transposase-Accessible Chromatin with Visualization

            Yusuke Miyanari

 

8. STREAMING-Tag System: Technology to Enable Visualization of Transcriptional Activity and Subnuclear Localization of Specific Endogenous Genes

            Hiroaki Ohishi and Hiroshi Ochiai

 

9. Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts

            Akihiko Sakashita, Chikara Takeuchi, So Maezawa, and Satoshi H. Namekawa

 

10. A Method for Detection of Somatic LINE-1 Insertions at the Single Cell Level from Postmortem Human Brain

            Miki Bundo and Kazuya Iwamoto

 

11. Solubilization of Mouse Sperm Chromatin for Sequencing Analyses Using a Chaperon Protein

            Yuko Fukuda, Keishi Shintomi, Kosuke Yamaguchi, Yasuhiro Fujiwara, and Yuki Okada

 

Part III: Manipulation of the Epigenome: Platforms for Epigenome Editing

 

12. Efficient Targeted DNA Methylation with dCas9-Coupled DNMT3A-DNMT3L Methyltransferase

            Pavel Bashtrykov, Nivethika Rajaram, and Albert Jeltsch

 

13. Regulation of Gene Expression Using dCas9-SunTag Platforms

            Sumiyo Morita, Takuro Horii, and Izuho Hatada

 

14. Concatenated Coiled-Coil Tag for Highly Efficient, Small Molecule-Inducible Upregulation of Endogenous Mammalian Genes

            Tina Lebar and Roman Jerala

 

15. Design, Construction, and Validation of Targeted Gene Activation with TREE System in Human Cells

            Tetsushi Sakuma and Takashi Yamamoto

 

Part IV: Manipulation of the Epigenome: Inducible System for Epigenome Editing

 

16. A Split CRISPR–Cpf1 Platform for Inducible Gene Activation

            Takahiro Otabe, Yuta Nihongaki, and Moritoshi Sato

 

Part V: Manipulation of the Epigenome: Epigenetically Modified Animals

 

17. Targeted DNA Methylation in Mouse Early Embryos

            Taiga Yamazaki, Yu Hatano, Noritada Kobayashi, and Kazuo Yamagata

 

18. Generation of Epigenetic Disease Model Mice by Targeted Demethylation of the Epigenome

            Takuro Horii, Sumiyo Morita, and Izuho Hatada

 

19. In Vivo Tissue-Specific DNA Demethylation in Mouse Liver through a Hydrodynamic Tail Vein Injection

            Koshi Hashimoto and Nozomi Hanzawa

 

20. Targeted Manipulation of Histone Modification in Medaka Embryos

            Hiroto S. Fukushima, Hiroyuki Takeda, and Ryohei Nakamura