CpG Islands

Description

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. Front Matter ....Pages i-xi Front Matter ....Pages 1-1 CpG Islands: A Historical Perspective (Francisco Antequera, Adrian Bird)....Pages 3-13 Biochemical Identification of Nonmethylated DNA by BioCAP-Seq (Hannah K. Long, Nathan R. Rose, Neil P. Blackledge, Robert J. Klose)....Pages 15-29 Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation (Cristina Gómez-Martín, Ricardo Lebrón, José L. Oliver, Michael Hackenberg)....Pages 31-47 CpG Islands in Cancer: Heads, Tails, and Sides (Humberto J. Ferreira, Manel Esteller)....Pages 49-80 Front Matter ....Pages 81-81 Infinium DNA Methylation Microarrays on Formalin-Fixed, Paraffin-Embedded Samples (Sebastian Moran, Manel Esteller)....Pages 83-107 The Use of Methylation-Sensitive Multiplex Ligation-Dependent Probe Amplification for Quantification of Imprinted Methylation (Ana Monteagudo-Sánchez, Intza Garin, Guiomar Perez de Nanclares, David Monk)....Pages 109-121 The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data (Izaskun Mallona, Alberto Sierco, Miguel A. Peinado)....Pages 123-135 Methylation-Sensitive Amplification Length Polymorphism (MS-AFLP) Microarrays for Epigenetic Analysis of Human Genomes (Sergio Alonso, Koichi Suzuki, Fumiichiro Yamamoto, Manuel Perucho)....Pages 137-156 Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells (Massimiliano Manzo, Christina Ambrosi, Tuncay Baubec)....Pages 157-174 Experimental Design and Bioinformatic Analysis of DNA Methylation Data (Yulia Medvedeva, Alexander Shershebnev)....Pages 175-194 Front Matter ....Pages 195-195 Assay for Transposase Accessible Chromatin (ATAC-Seq) to Chart the Open Chromatin Landscape of Human Pancreatic Islets (Helena Raurell-Vila, Mireia Ramos-Rodríguez, Lorenzo Pasquali)....Pages 197-208 Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq) (Suhn Kyong Rhie, Shannon Schreiner, Peggy J. Farnham)....Pages 209-229 Genome-Wide Mapping of Protein–DNA Interactions on Nascent Chromatin (Chenhuan Xu, Victor G. Corces)....Pages 231-238 Analysis of Chromatin Interactions Mediated by Specific Architectural Proteins in Drosophila Cells (Masami Ando-Kuri, I. Sarahi M. Rivera, M. Jordan Rowley, Victor G. Corces)....Pages 239-256 High-Throughput Single-Cell RNA Sequencing and Data Analysis ( Sagar, Josip Stefan Herman, John Andrew Pospisilik, Dominic Grün)....Pages 257-283 Functional Insulator Scanning of CpG Islands to Identify Regulatory Regions of Promoters Using CRISPR (Alice Grob, Masue Marbiah, Mark Isalan)....Pages 285-301 An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics (Eleni Gelali, Joaquin Custodio, Gabriele Girelli, Erik Wernersson, Nicola Crosetto, Magda Bienko)....Pages 303-333 Back Matter ....Pages 335-340