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. Corrêa 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

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. Szabó

13. Immunochemical Detection of Modified Cytosine Species in Lampbrush Chromatin

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-Ca