DNA Methylation Protocols

This third edition volume expands on the previous editions by providing a comprehensive update on the available technologies required to successfully perform DNA methylation analysis. The different technologies discussed in this book analyze the global DNA methylation contents, comprehensive analyses using various NGS based methods for genome-wide DNA methylation analysis, along with precise quantification of DNA methylation levels on single CpG positions. The chapters in this book are divided into 7 parts: an introduction to the field along with tips on study design and data analysis; global DNA methylation levels; genome-wide DNA methylation analysis; highly multiplexed target regions; locus-specific DNA methylation analysis; DNA methylation analysis of specific biological samples; and hydroxymethylation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materialsand reag ents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and thorough, DNA Methylation Protocols, Third Edition is a valuable resource for postdoctoral investigators and research scientists who work with different aspects of genetics, and cellular and molecular biology, as well as clinicians who are involved in diagnostics or treatment of diseases with epigenetic components.

Inhaltsverzeichnis:

A Summary of the Biological Processes, Disease-Associated Changes and Clinical Applications of DNA Methylation.- Considerations for Design and Analysis of DNA Methylation Studies.- Quantification of Global DNA Methylation Levels by Mass Spectrometry.- Antibody Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections and Mammaliam Embryos.- Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq Protocol.- Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing.- Post-Bisulfite Adaptor Tagging for PCR-Free Whole-Genome Bisulfite Sequencing.- Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size Selection.- Low Input Whole-Genome Bisulfite Sequencing Using a Post-Bisulfite Adapter Tagging Approach.- Methyl-CpG Binding Domain Sequencing: MBD-seq.- The HELP-Based Assays.- Comprehensive Whole DNA Methylome Analysis by InDigital Restriction Enzyme Analysis of Methylation (DREAM).- N ucleosome Occupancy and Methylome Sequencing (NOMe-seq).- Bisulfite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq).- A Guide to Illumina BeadChip Data Analysis.- Microdroplet PCR for Highly-Multiplexed Targeted Bisulfite Sequencing.- Multiplexed DNA Methylation Analysis of Target Regions Using Microfluidics (Fluidigm).- Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock Probes.- Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment System.- Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes MSRE-qPCR.- Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing®.- Methylation-Specific PCR.- Quantitation of DNA Methylation by Quantitative Multiplex Methylation-Specific PCR (QM-MSP).- MethyLight and Digital MethyLight.- Quantitative Region-Specific DNA Methylation Analysis by the EPITYPERTM Technology.- Methylation-Specific Multiplex Ligation-Dependent Probe Amplificat ion (MS-MLPA).- Methylation - Sensitive - High Resolution Melting (MS-HRM).- Hairpin Bisulfite Sequencing: Synchronous Methylation Analysis on Complementary DNA Strands of Individual Chromosomes.- Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA Sequences.- DNA Methylation Analysis from Blood Spots: Increasing Yield and Quality for Genome-Wide and Locus-Specific Methylation.- DNA Methylation Analysis of Free-Circulating DNA in Body Fluids.- Tet-Assisted Bisulfite Sequencing (TAB-seq).- Multiplexing for Oxidative Bisulfite Sequencing (oxBS-seq).- Affinity-Based Enrichment Techniques for the Genome-Wide Analysis of 5-Hydroxymethylcytosine.