Ruzov Alexey, Gering Martin. (eds.) DNA Modifications: Methods and Protocols

Humana Press, 2021. — 495 p. — ISBN: 1071608754This book provides an overview of methods and experimental protocols that are currently used to analyze the presence and abundance of non-canonical DNA nucleotides in different biological systems. Focusing particularly on the newly discovered and less studied DNA modifications that are enzymatically produced and are likely to play specific roles in various biological processes, the volume explores chromatography- and mass spectrometry-based techniques for the detection and quantification of DNA modifications, antibody-based approaches to study their spatial distribution in different cells and tissues, and methods to analyze their genomic distribution with the help of bioinformatics tools that interrogate the corresponding datasets. 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Authoritative and comprehensive, DNA Modifications: Methods and Protocols serves as an ideal guide to research scientists and PhD students in this rapidly developing discipline, and, thus, will ultimately contribute to deciphering the roles of non-canonical DNA nucleotides in different biological systems.Table of contents (34 chapters)
Modified Forms of Cytosine in Eukaryotes: DNA (De)methylation and Beyond
Evidence for Noncytosine Epigenetic DNA Modifications in Multicellular Eukaryotes: An Overview
Mass Spectrometry-Based Analysis of DNA Modifications: Potential Applications in Basic Research and Clinic
Mapping DNA Methylation in Mammals: The State of the Art
Detection of Modified Bases in Bacteriophage Genomic DNA
Liquid Chromatography–Mass Spectrometry Analysis of Cytosine Modifications
Detection of DNA Methylation in Genomic DNA by UHPLC-MS/MS
Quantification of DNA Modifications Using Two-Dimensional Ultraperformance Liquid Chromatography Tandem Mass Spectrometry (2D-UPLC-MS/MS)
MS Analysis of DNA Modifications in Urinary/Body Fluids
Preparation of Internal Standards for 2D-UPLC-MS/MS Quantification of Noncanonical DNA Bases
Detection of TET-Oxidized 5-Methylcytosine Bases by Capillary Gel Electrophoresis
Immunochemical Detection of Modified Cytosine Species in Mammalian Preimplantation Embryos
Immunochemical Detection of Modified Cytosine Species in Lampbrush Chromatin
Detection of Low-Abundance DNA Modifications Using Signal Amplification-Based Immunocytochemistry
Immunohistochemical Detection of Modified Cytosine Bases in Rodent Brain
Immunohistochemical Detection of 5-Hydroxymethylcytosine and 5-Carboxylcytosine in Sections of Zebrafish Embryos
Immunochemical Detection of Modified Species of Cytosine in Plant Tissues
Antigen Retrieval for Immunostaining of Modified Cytosine Species
Computational Analysis of DNA Modifications in Confocal Images
Three-Dimensional Confocal Analysis of Chromosome Positioning Coupled with Immunofluorescence in Mouse Sperm Nuclei
Analysis of 5-Hydroxymethyluracil Levels Using Flow Cytometry
Hairpin-Bisulfite PCR
Genome-Wide Mapping of DNA Methylation 5mC by Methylated DNA Immunoprecipitation (MeDIP)-Sequencing
Analysis of 5-Carboxylcytosine Distribution Using DNA Immunoprecipitation
High-Resolution Analysis of 5-Hydroxymethylcytosine by TET-Assisted Bisulfite Sequencing
Oxidative Bisulfite Sequencing: An Experimental and Computational Protocol
Bisulfite-Free Sequencing of 5-Hydroxymethylcytosine with APOBEC-Coupled Epigenetic Sequencing (ACE-Seq)
Single-Nucleotide-Resolution Sequencing of N6-Methyldeoxyadenosine
Design and Application of DNA Modification-Specific Transcription-Activator-Like Effectors
Notes on Functional Modules in the Assembly of CRISPR/Cas9-Mediated Epigenetic Modifiers
Analyzing DNA-Immunoprecipitation Sequencing Data
Bioinformatics Analysis of DNA Methylation Through Bisulfite Sequencing Data
Unified Analysis of Multiple ChIP-Seq Datasets
Integrated Analysis of DNA Methylation, Hydroxymethylation, and Gene Expression Data Using ME-Class2