Includes cutting-edge techniques
Provides step-by-step detail essential for reproducible results
Contains key implementation advice from the experts
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.
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 Tranillegalscriptional 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
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.
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.
DNA Methylation Analysis Using Bisulfite Pyrosequencing.- Post-Bisulfite Adaptor Tagging Based on an ssDNA Ligation Technique (tPBAT).- Reduced Representation Bisulfite Sequencing (RRBS).- Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers.- ATAC-Seq Analysis of Accessible Chromatin: From Experimental Steps to Data Analysis.- Low-Input CUT&RUN for Mouse Oocytes and Preimplantation Embryos.- Imaging Chromatin Accessibility by Assay of Transposase-Accessible Chromatin with Visualization.- STREAMING-Tag System: Technology to Enable Visualization of Tranillegalscriptional Activity and Subnuclear Localization of Specific Endogenous Genes.- Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts.- A Method for Detection of Somatic LINE-1 Insertions at the Single Cell Level from Postmortem Human Brain.- Solubilization of Mouse Sperm Chromatin for Sequencing Analyses Using a Chaperon Protein.- Efficient Targeted DNA Methylation with dCas9-Coupled DNMT3A-DNMT3L Methyltransferase.- Regulation of Gene Expression Using dCas9-SunTag Platforms.- Concatenated Coiled-Coil Tag for Highly Efficient, Small Molecule-Inducible Upregulation of Endogenous Mammalian Genes.- Design, Construction, and Validation of Targeted Gene Activation with TREE System in Human Cells.- A Split CRISPR-Cpf1 Platform for Inducible Gene Activation.- Targeted DNA Methylation in Mouse Early Embryos.- Generation of Epigenetic Disease Model Mice by Targeted Demethylation of the Epigenome.- In Vivo
Tissue-Specific DNA Demethylation in Mouse Liver through a Hydrodynamic Tail Vein Injection.- Targeted Manipulation of Histone Modification in Medaka Embryos.
Inhaltsverzeichnis
DNA Methylation Analysis Using Bisulfite Pyrosequencing.- Post-Bisulfite Adaptor Tagging Based on an ssDNA Ligation Technique (tPBAT).- Reduced Representation Bisulfite Sequencing (RRBS).- Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers.- ATAC-Seq Analysis of Accessible Chromatin: From Experimental Steps to Data Analysis.- Low-Input CUT&RUN for Mouse Oocytes and Preimplantation Embryos.- Imaging Chromatin Accessibility by Assay of Transposase-Accessible Chromatin with Visualization.- STREAMING-Tag System: Technology to Enable Visualization of Tranillegalscriptional Activity and Subnuclear Localization of Specific Endogenous Genes.- Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts.- A Method for Detection of Somatic LINE-1 Insertions at the Single Cell Level from Postmortem Human Brain.- Solubilization of Mouse Sperm Chromatin for Sequencing Analyses Using a Chaperon Protein.- Efficient Targeted DNA Methylation with dCas9-Coupled DNMT3A-DNMT3L Methyltransferase.- Regulation of Gene Expression Using dCas9-SunTag Platforms.- Concatenated Coiled-Coil Tag for Highly Efficient, Small Molecule-Inducible Upregulation of Endogenous Mammalian Genes.- Design, Construction, and Validation of Targeted Gene Activation with TREE System in Human Cells.- A Split CRISPR-Cpf1 Platform for Inducible Gene Activation.- Targeted DNA Methylation in Mouse Early Embryos.- Generation of Epigenetic Disease Model Mice by Targeted Demethylation of the Epigenome.- In Vivo Tissue-Specific DNA Demethylation in Mouse Liver through a Hydrodynamic Tail Vein Injection.- Targeted Manipulation of Histone Modification in Medaka Embryos.
Klappentext
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.
