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 Transcriptional 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.

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.

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