CpG Islands

1. Front Matter

   Pages i-xi

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2. Sequence and Other Properties of CpG Islands

   1. Front Matter

      Pages 1-1

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   2. CpG Islands: A Historical Perspective

      • Francisco Antequera, Adrian Bird

      Pages 3-13

   3. Biochemical Identification of Nonmethylated DNA by BioCAP-Seq

      • Hannah K. Long, Nathan R. Rose, Neil P. Blackledge, Robert J. Klose

      Pages 15-29

   4. 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

   5. CpG Islands in Cancer: Heads, Tails, and Sides

      • Humberto J. Ferreira, Manel Esteller

      Pages 49-80

3. Methods for the Measurement of DNA Methylation at CpG Islands

   1. Front Matter

      Pages 81-81

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   2. Infinium DNA Methylation Microarrays on Formalin-Fixed, Paraffin-Embedded Samples

      • Sebastian Moran, Manel Esteller

      Pages 83-107

   3. 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

   4. The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data

      • Izaskun Mallona, Alberto Sierco, Miguel A. Peinado

      Pages 123-135

   5. 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

   6. Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells

      • Massimiliano Manzo, Christina Ambrosi, Tuncay Baubec

      Pages 157-174

   7. Experimental Design and Bioinformatic Analysis of DNA Methylation Data

      • Yulia Medvedeva, Alexander Shershebnev

      Pages 175-194

4. Chromatin and Related Genomics Methods Used for Understanding the Functional Role of CpG Islands and Other Regulatory Regions

   1. Front Matter

      Pages 195-195

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   2. 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

   3. 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

   4. Genome-Wide Mapping of Protein–DNA Interactions on Nascent Chromatin

      • Chenhuan Xu, Victor G. Corces

      Pages 231-238

   5. 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

   6. High-Throughput Single-Cell RNA Sequencing and Data Analysis

      • Sagar, Josip Stefan Herman, John Andrew Pospisilik, Dominic Grün

      Pages 257-283

   7. Functional Insulator Scanning of CpG Islands to Identify Regulatory Regions of Promoters Using CRISPR

      • Alice Grob, Masue Marbiah, Mark Isalan

      Pages 285-301

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.

• CpG dinucleotides
• Gene regulation
• Bioinformatics
• Computational methods
• DNA methylation
• Epigenetics
• Chromatin interactions

• Josep Carreras Leukaemia, Research Institute, Badalona, Spain

  Tanya Vavouri

• IGTP, IMPPC, Badalona, Spain

  Miguel A. Peinado

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