This practical collection examines methodologies originating from the benefits of genome-wide approaches to studying epigenetics, which has opened the emerging field of epigenomics. Focusing on the areas of cancer, inflammatory and autoimmune disorders, chapters discuss three main components of the epigenome and their role in the regulation of gene expression and present a detailed method section specific to studying each component, including data analyses, troubleshooting, and feasibility in different experimental settings. The main topics are high-throughput and targeted methods for DNA methylation analysis, nucleosome position mapping, studying epigenetic effects of gut microbiota, optical imaging for detection of epigenetic aberrations in living cells, methods for microRNA, and histone code profiling. Written for the Methods in Pharmacology and Toxicology series, the book includes the kind of detail and implementation advice to encourage success in the lab.
Authoritative and easily applicable, Epigenetics and Gene Expression in Cancer, Inflammatory and Immune Diseases aims to provide pharmacologists, molecular biologists, bioinformaticians, and toxicologists with a vital background on epigenetics and state-of-the-art techniques in epigenomics.
Table of contents (11 protocols)
Pages i-xii
High-Throughput Techniques for DNA Methylation Profiling
Sophie Petropoulos, David Cheishvili, Moshe Szyf
Pages 1-15
Reduced Representation Bisulfite Sequencing (RRBS) and Cell Sorting Prior to DNA Methylation Analysis in Psychiatric Disorders
Wilfred C. de Vega, Atif Hussain, Patrick O. McGowan
Pages 17-32
Targeted DNA Methylation Analysis Methods
David Cheishvili, Sophie Petropoulos, Steffan Christiansen, Moshe Szyf
Pages 33-50
Analyzing Targeted Nucleosome Position and Occupancy in Cancer, Obesity, and Diabetes
Prasad P. Devarshi, Tara M. Henagan
Pages 51-62
Synthesis and Application of Cell-Permeable Metabolites for Modulating Chromatin Modifications Regulated by α-Ketoglutarate-Dependent Enzymes
Hunter T. Balduf, Antonella Pepe, Ann L. Kirchmaier
Pages 63-79
High-Throughput Screening of Small Molecule Transcriptional Regulators in Embryonic Stem Cells Using qRT-PCR
Emily C. Dykhuizen, Leigh C. Carmody, Nicola J. Tolliday
Pages 81-95
Methods for MicroRNA Profiling in Cancer
Sushuma Yarlagadda, Anusha Thota, Ruchi Bansal, Jason Kwon, Murray Korc, Janaiah Kota
Pages 97-113
Microbiota and Epigenetic Regulation of Inflammatory Mediators
Marlene Remely, Heidrun Karlic, Irene Rebhan, Martina Greunz, Alexander G. Haslberger
Pages 115-134
Optical Microscopy and Spectroscopy for Epigenetic Modifications in Single Living Cells
Yi Cui, Joseph Irudayaraj
Pages 135-154
MicroRNAs in Therapy and Toxicity
David J. MacEwan, Niraj M. Shah, Daniel J. Antoine
Pages 155-167
Genetics and Epigenetics of Multiple Sclerosis
Borut Peterlin, Ales Maver, Vidmar Lovro, Luca Lovrečić
Pages 169-192
