Main 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.

Contents:

Part I: Sequence and Other Properties of CpG Islands

1. CpG Islands: A Historical Perspective

Francisco Antequera and Adrian Bird

2. Biochemical Identification of Non-Methylated DNA by BioCAP-Seq

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

3. Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation

Cristina Gomez-Martin, Ricardo Lebron, Jose L. Oliver, and Michael Hackenberg

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

Humberto J. Ferreira and Manel Esteller

Part II: Methods for the Measurement of DNA Methylation at CpG Islands

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

Sebastian Moran and Manel Esteller

6. The Use of Methylation-Sensitive Multiplex Ligation-Dependent Probe Amplification for Quantification of Imprinted Methylation

Ana Monteagudo-Sa nchez, Intza Garin, Guiomar Perez de Nanclares, and David Monk

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

Izaskun Mallona, Alberto Sierco, and Miguel A. Peinado

8. Methylation-Sensitive Amplification Length Polymorphism (MS-AFLP) Microarrays for Epigenetic Analysis of Human Genomes

Sergio Alonso, Koichi Suzuki, Fumiichiro Yamamoto, and Manuel Perucho

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

Massimiliano Manzo, Christina Ambrosi, and Tuncay Baubec

10. Experimental Design and Bioinformatic Analysis of DNA Methylation Data

Yulia Medvedeva and Alexander Shershebnev

Part III: Chromatin and Related Genomics Methods Used for Understanding the Functional Role of CpG Islands and Other Regulatory Regions

11. Assay for Transposase Accessible Chromatin (ATAC-Seq) to Chart the Open Chromatin Landscape of Human Pancreatic Islets

Helena Raurell-Vila, Mireia Ramos-Rodriguez, and Lorenzo Pasquali

12. Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq)

Suhn Kyong Rhie, Shannon Schreiner, and Peggy J. Farnham

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

Chenhuan Xu and Victor G. Corces

14. Analysis of Chromatin Interactions Mediated by Specific Architectural Proteins in Drosophila Cells

Masami Ando-Kuri, I. Sarahi M. Rivera, M. Jordan Rowley, and Victor G. Corces

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

Sagar, Josip Stefan Herman, John Andrew Pospisilik, and Dominic Grun

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

Alice Grob, Masue Marbiah, and Mark Isalan

17. An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics

Eleni Gelali, Joaquin Custodio, Gabriele Girelli, Erik Wernersson, Nicola Crosetto, and Magda Bienko