Cpg Islands: Methods and Protocols (Hardcover, 2018)

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