DNA Modifications: Methods and Protocols

ISBN-13: 9781071608784 / Angielski / Miękka / 2021 / 495 str.

Alexey Ruzov; Martin Gering

Spis treści

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

            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. Szabó

 

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, Joëlle Henry-Berger, Joël 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 Stöger

 

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. Szabó, 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, Álvaro Muñoz-López, 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

Blurb

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.