CpG Islands

This detailed volume examines bioinformatic and molecular biological methods useful to identify and to explore the functions of CpG islands, key navigation points to understand gene regulation in fundamental processes such as development and cell differentiation as well as in diseases like cancer. Beginning with a historical perspective and important properties of CpG islands, the book continues with sections on computational and wet lab methods related to the study of DNA methylation, and in-depth protocols for the analysis of CpG island functional features including epigenetic profiling and chromatin interactions. 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, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, CpG Islands: Methods and Protocols aims to provide readers with the information and methodologies necessary to continue to decipher how a genome's structure and organization contribute to regulate biological processes.

Includes cutting-edge techniques for the study of CpG islands Provides step-by-step detail essential for reproducible results Contains key implementation advice from the experts

Inhalt

CpG Islands: A Historical Perspective.- Biochemical Identification of Non-Methylated DNA by BioCAP-Seq.- Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation.- CpG Islands in Cancer: Heads, Tails, and Sides.- Infinium DNA Methylation Microarrays on Formalin-Fixed Paraffin-Embedded Samples.- The Use of Methylation-Sensitive Multiplex Ligation-Dependent Probe Amplification for Quantification of Imprinted Methylation.- The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data.- Methylation-Sensitive Amplification Length Polymorphism (MS-AFLP) Microarrays for Epigenetic Analysis of Human Genomes.- Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells.- Experimental Design and Bioinformatic Analysis of DNA Methylation Data.- Assay for Transposase Accessible Chromatin (ATAC-Seq) to Chart the Open Chromatin Landscape of Human Pancreatic Islets.- Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq).- Genome-Wide Mapping of Protein-DNA Interactions on Nascent Chromatin.- Analysis of Chromatin Interactions Mediated by Specific Architectural Proteins in Drosophila Cells.- High-Throughput Single-Cell RNA Sequencing and Data Analysis.- Functional Insulator Scanning of CpG Islands to Identify Regulatory Regions of Promoters Using CRISPR.- An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics.