Cancer Epigenetics by Dhasarathy, Archana; Takaku, Motoki;

Long description:

This detailed volume explores tools to study epigenetics in cancer and to manipulate the proteins involved, critical to our understanding of mechanisms in cancer initiation and progression. This book compiles protocols for detecting core epigenetic modifications including DNA methylation, histone modifications, highlighting chromatin immunoprecipitation (ChIP), CUT&RUN, and advanced microscopy for visualizing chromatin architecture in situ. Additionally, it features chromatin accessibility protocols, methods to detect long non-coding RNAs and microRNAs from challenging clinical samples, and more. 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 and readily reproducible laboratory protocols, as well as tips for troubleshooting and avoiding known pitfalls.

Authoritative and practical, Cancer Epigenetics: Methods and Protocols serves as a practical resource for researchers at all stages on their journey to unlock the secrets of cancer epigenomes, and ultimately, to improve patient outcomes.

Chapter 5 is available open access under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License via link.springer.com.

Table of Contents:

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Enzymatic, Nondestructive Sequencing of 5-Methylcytosine with Direct Methylation Sequencing (DM-Seq).- FENGC: Targeted, Multiplexed, and Integrated Single-Molecule Profiling of Chromatin Accessibility and DNA Methylation.- Chromatin Immunoprecipitation Sequencing in Cancer Cells.- Chromatin Immunoprecipitation from Mouse Lung Tissue.- High-Efficiency Genomic Mapping of Chromatin-Associated Targets with CUT&RUN.- CUT&Tag for Chromatin Profiling in Cancer Tissue.- Assay for Transposase-Accessible Chromatin Sequencing (ATAC-Seq) of Cancer Cells in Culture.- Investigating the Physiologic Regulation of Transposable Elements In Vivo: Nuclei Preparation from Primary Mouse Tissues for Epigenomic Analyses and Computational Approaches to Interrogate the Repeat Genome.- Single Molecule Tracking: Visualizing Transcription of Endogenous Loci in Living Cells.- Advanced High-Resolution and Super-Resolution Microscopy Techniques for Investigating Chromatin Structure and Epigenetics.- A Framework for Analyzing the Epigenetic and Transcriptomic Landscape of Cancers Using Single Cell Multiomic Data.- A Comprehensive Pipeline for Long Non-Coding RNA Discovery and Characterization in Cancer.- Small RNA Analysis in Cancer Cells.- Isolation of RNA and MicroRNAs from Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) and Cultured Cells for Subsequent Applications.- Dissecting Epigenetic Drug Response Mechanisms Using CRISPR Knockout Screens.- Tools for Cancer Research: CRISPR/Cas-Based Gene Editing and Auxin-Induced Degron Systems.- The High Throughput C-Circle Assay for Identifying Modulators of Alternative Lengthening of Telomeres (ALT) Activity.- Cell-Free DNA-Based Methods to Map Chromatin.- MicroRNA Extraction from Extracellular Vesicles by Nanowire Devices.