Preface
Contributors
Part I Introduction
1 Modified Forms of Cytosine in Eukaryotes: DNA
(De)methylation and Beyond 3
Maria Eleftheriou and Alexey Ruzov
2 Evidence for Noncytosine Epigenetic DNA Modifications
in Multicellular Eukaryotes: An Overview 15
Paige Lowe, Ryszard Olinski, and Alexey Ruzov
3 Mass Spectrometry-Based Analysis of DNA Modifications:
Potential Applications in Basic Research and Clinic 27
Ryszard Olinski, Rafal Rozalski, and Daniel Gackowski
4 Mapping DNA Methylation in Mammals: The State of the Art 37
Antonio Lentini and Colm E. Nestor
Part II D etection and Quantification of DNA
Modifications Using Mass Spectrometry
and Capillary Gel Electrophoresis
5 Detection of Modified Bases in Bacteriophage Genomic DNA 53
Yan-Jiun Lee and Peter R. Weigele
6 Liquid Chromatography–Mass Spectrometry Analysis
of Cytosine Modifications 67
Nan Dai and Ivan R. Corrêa Jr
7 Detection of DNA Methylation in Genomic DNA
by UHPLC-MS/MS 79
Konstantinos Boulias and Eric Lieberman Greer
8 Quantification of DNA Modifications Using Two-Dimensional
Ultraperformance Liquid Chromatography Tandem
Mass Spectrometry (2D-UPLC-MS/MS) 91
Marta Starczak, Maciej Gawronski, Ryszard Olinski, and Daniel Gackowski
9 MS Analysis of DNA Modifications in Urinary/Body Fluids 109
Aleksandra Skalska, Agnieszka Siomek-Gorecka, Ryszard Olinski,
and Rafal Rozalski
10 Preparation of Internal Standards for 2D-UPLC-MS/MS
Quantification of Noncanonical DNA Bases 123
Marta Starczak, Aleksandra Skalska, Rafal Rozalski, Ryszard Olinski,
and Daniel Gackowski
11 Detection of TET-Oxidized 5-Methylcytosine Bases by Capillary
Gel Electrophoresis 137
Romualdas Vaisvila, Lise Hunault, and Lana Saleh
Part III A ssessing the Levels and Spatial Distribution
of DNA Modifications Using Antibody-Based Approaches
12 Immunochemical Detection of Modified Cytosine Species
in Mammalian Preimplantation Embryos 147
Tie-Bo Zeng and Piroska E. Szabó
13 Immunochemical Detection of Modified Cytosine Species
in Lampbrush Chromatin 159
Garry T. Morgan
14 Detection of Low-Abundance DNA Modifications Using
Signal Amplification-Based Immunocytochemistry 169
Abdulkadir Abakir and Alexey Ruzov
15 Immunohistochemical Detection of Modified Cytosine
Bases in Rodent Brain 183
Marcus D. Wallis and Rebecca C. Trueman
16 Immunohistochemical Detection of 5-Hydroxymethylcytosine
and 5-Carboxylcytosine in Sections of Zebrafish Embryos 193
Peter Jessop and Martin Gering
17 Immunochemical Detection of Modified Species of Cytosine
in Plant Tissues 209
Marcos Viejo, Igor Yakovlev, and Carl Gunnar Fossdal
18 Antigen Retrieval for Immunostaining of Modified Cytosine Species 217
Selcen Celik-Uzuner
19 Computational Analysis of DNA Modifications in Confocal Images 227
Seema Rajani, Christopher Gell, Abdulkadir Abakir, and Robert Markus
20 Three-Dimensional Confocal Analysis of Chromosome
Positioning Coupled with Immunofluorescence in Mouse Sperm Nuclei 255
Alexandre Champroux, Chantal Goubely, Joëlle Henry-Berger,
Joël R. Drevet, and Ayhan Kocer
21 Analysis of 5-Hydroxymethyluracil Levels Using Flow Cytometry 269
Lidia Gackowska, Anna Labejszo, and Daniel Gackowski
Part IVMapping DNA Modifications
22 Hairpin-Bisulfite PCR 287
Reinhard Stöger
23 Genome-Wide Mapping of DNA Methylation 5mC by Methylated
DNA Immunoprecipitation (MeDIP)-Sequencing 301
Millissia Ben Maamar, Ingrid Sadler-Riggleman, Daniel Beck,
and Michael K. Skinner
24 Analysis of 5-Carboxylcytosine Distribution Using DNA
Immunoprecipitation 311
Abdulkadir Abakir, Fahad Alenezi, and Alexey Ruzov
i25 High-Resolution Analysis of 5-Hydroxymethylcytosine
by TET-Assisted Bisulfite Sequencing 321
Zhijun Huang, Yingying Meng, Piroska E. Szabó, Rahul M. Kohli,
and Gerd P. Pfeifer
26 Oxidative Bisulfite Sequencing: An Experimental and Computational
Protocol 333
Marie De Borre and Miguel R. Branco
27 Bisulfite-Free Sequencing of 5-Hydroxymethylcytosine
with APOBEC-Coupled Epigenetic Sequencing (ACE-Seq) 349
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 VA pplications of Genome Targeting Methods
in Epigenetics
29 Design and Application of DNA Modification-Specific
Transcription-Activator-Like Effectors 381
Benjamin Buchmuller, Álvaro Muñoz-López, Mario Gieß,
and Daniel Summerer
30 Notes on Functional Modules in the Assembly of CRISPR/Cas9-Mediated
Epigenetic Modifiers 401
Alexander Kondrashov and Elena Karpova
Part VI A nalysis of DNA Modifications Sequencing Datasets
31 Analyzing DNA-Immunoprecipitation Sequencing Data 431
Antonio Lentini and Colm E. Nestor
32 Bioinformatics Analysis of DNA Methylation Through Bisulfite
Sequencing Data 441
Fei Sang
33 Unified Analysis of Multiple ChIP-Seq Datasets 451
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 467
Manoj K. Singh and John R. Edwards
Index 491
DNA Modifications Methods and Protocols PDF Ebook
