DNA modifications : methods and protocols
Author(s)
Bibliographic Information
DNA modifications : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2198）
Humana Press, 2021
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Note
Includes bibliographical references and index
Description and Table of Contents
Description
This 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
Part I: Introduction
1. Modified Forms of Cytosine in Eukaryotes: DNA (De)Methylation and Beyond
Maria Eleftheriou and Alexey Ruzov
2. Evidence for Non-Cytosine Epigenetic DNA Modifications in Multicellular Eukaryotes: An Overview
Paige Lowe, Ryszard Olinski, and Alexey Ruzov
3. Mass Spectrometry-Based Analysis of DNA Modifications: Potential Applications in Basic Research and Clinic
Ryszard Olinski, Rafal Rozalski, and Daniel Gackowski
4. Mapping DNA Methylation in Mammals: The State of the Art
Antonio Lentini and Colm E. Nestor
Part II: Detection and Quantification of DNA Modifications Using Mass Spectrometry and Capillary Gel Electrophoresis
5. Detection of Modified Bases in Bacteriophage Genomic DNA
Yan-Jiun Lee and Peter R. Weigele
6. Liquid Chromatography-Mass Spectrometry Analysis of Cytosine Modifications
Nan Dai and Ivan R. Correa Jr.
7. Detection of DNA Methylation in Genomic DNA by UHPLC-MS/MS
Konstantinos Boulias and Eric Lieberman Greer
8. Quantification of DNA Modifications Using Two-Dimensional Ultra-Performance Liquid Chromatography Tandem Mass-Spectrometry (2D-UPLC-MS/MS)
Marta Starczak, Maciej Gawronski, Ryszard Olinski, and Daniel Gackowski
9. MS Analysis of DNA Modifications in Urinary/Body Fluids
Aleksandra Skalska, Agnieszka Siomek-Gorecka, Ryszard Olinski, and Rafal Rozalski
10. Preparation of Internal Standards for 2D-UPLC-MS/MS Quantification of Non-Canonical DNA Bases
Marta Starczak, Aleksandra Skalska, Rafal Rozalski, Ryszard Olinski, and Daniel Gackowski
11. Detection of TET-Oxidized 5-Methylcytosine Bases by Capillary Gel Electrophoresis
Romualdas Vaisvila, Lise Hunault, and Lana Saleh
Part III: Assessing the Levels and Spatial Distribution of DNA Modifications Using Antibody-Based Approaches
12. Immunochemical Detection of Modified Cytosine Species in Mammalian Preimplantation Embryos
Tie-Bo Zeng and Piroska E. Szabo
13. Immunochemical Detection of Modified Cytosine Species in Lampbrush Chromatin
Garry T. Morgan
14. Detection of Low-Abundance DNA Modifications Using Signal Amplification-Based Immunocytochemistry
Abdulkadir Abakir and Alexey Ruzov
15. Immunohistochemical Detection of Modified Cytosine Bases in Rodent Brain
Marcus D. Wallis and Rebecca C. Trueman
16. Immunohistochemical Detection of 5-Hydroxymethylcytosine and 5-Carboxylcytosine in Sections of Zebrafish Embryos
Peter Jessop and Martin Gering
17. Immunochemical Detection of Modified Species of Cytosine in Plant Tissues
Marcos Viejo, Igor Yakovlev, and Carl Gunnar Fossdal
18. Antigen Retrieval for Immunostaining of Modified Cytosine Species
Selcen Celik-Uzuner
19. Computational Analysis of DNA Modifications in Confocal Images
Seema Rajani, Christopher Gell, Abdulkadir Abakir, and Robert Markus
20. Three-Dimensional Confocal Analysis of Chromosome Positioning Coupled with Immunofluorescence in Mouse Sperm Nuclei
Alexandre Champroux, Chantal Goubely, Joelle Henry-Berger, Joel R. Drevet, and Ayhan Kocer
21. Analysis of 5-Hydroxymethyluracil Levels Using Flow Cytometry
Lidia Gackowska, Anna Labejszo, and Daniel Gackowski
Part IV: Mapping DNA Modifications
22. Hairpin-Bisulfite PCR
Reinhard Stoeger
23. Genome-Wide Mapping of DNA Methylation 5mC by Methylated DNA Immunoprecipitation (MeDIP)-Sequencing
Millissia Ben Maamar, Ingrid Sadler-Riggleman, Daniel Beck, and Michael K. Skinner
24. Analysis of 5-Carboxylcytosine Distribution Using DNA Immunoprecipitation
Abdulkadir Abakir, Fahad Alenezi, and Alexey Ruzov
25. High Resolution Analysis of 5-Hydroxymethylcytosine by TET-Assisted Bisulfite Sequencing
Zhijun Huang, Yingying Meng, Piroska E. Szabo, Rahul M. Kohli, and Gerd P. Pfeifer
26. Oxidative Bisulfite Sequencing: An Experimental and Computational Protocol
Marie De Borre and Miguel R. Branco
27. Bisulfite-Free Sequencing of 5-Hydroxymethylcytosine with APOBEC-Coupled Epigenetic Sequencing (ACE-Seq)
Tong Wang, Meiqi Luo, Kiara N. Berrios, Emily K. Schutsky, Hao Wu, and Rahul M. Kohli
28. Single-Nucleotide-Resolution Sequencing of N6-Methyldeoxyadenosine
Wee Siong Sho Goh
Part V: Applications of Genome Targeting Methods in Epigenetics
29. Design and Application of DNA Modification-Specific Transcription-Activator-Like Effectors
Benjamin Buchmuller, Alvaro Munoz-Lopez, Mario Giess, and Daniel Summerer
30. Notes on Functional Modules in the Assembly of CRISPR/Cas9-Mediated Epigenetic Modifiers
Alexander Kondrashov and Elena Karpova
Part VI: Analysis of DNA Modifications Sequencing Datasets
31. Analyzing DNA-Immunoprecipitation Sequencing Data
Antonio Lentini and Colm E. Nestor
32. Bioinformatics Analysis of DNA Methylation through Bisulfite Sequencing Data
Fei Sang
33. Unified Analysis of Multiple ChIP-Seq Datasets
Gang Ma, Isaac A. Babarinde, Qiang Zhuang, and Andrew P. Hutchins
34. Integrated Analysis of DNA Methylation, Hydroxymethylation, and Gene Expression Data Using ME-Class2
Manoj K. Singh and John R. Edwards
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