Description
Springer Dna Modifications Methods And Protocols 2021 Edition by Ruzov A.
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. _x000D_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._x000D_ Table of contents :- Part I: Introduction1. Modified Forms of Cytosine in Eukaryotes: DNA (De)Methylation and BeyondMaria Eleftheriou and Alexey Ruzov2. Evidence for Non-Cytosine Epigenetic DNA Modifications in Multicellular Eukaryotes: An OverviewPaige Lowe, Ryszard Olinski, and Alexey Ruzov3. Mass Spectrometry-Based Analysis of DNA Modifications: Potential Applications in Basic Research and ClinicRyszard Olinski, Rafal Rozalski, and Daniel Gackowski4. Mapping DNA Methylation in Mammals: The State of the ArtAntonio Lentini and Colm E. NestorPart II: Detection and Quantification of DNA Modifications Using Mass Spectrometry and Capillary Gel Electrophoresis5. Detection of Modified Bases in Bacteriophage Genomic DNAYan-Jiun Lee and Peter R. Weigele6. Liquid Chromatography-Mass Spectrometry Analysis of Cytosine ModificationsNan Dai and Ivan R. Correa Jr.7. Detection of DNA Methylation in Genomic DNA by UHPLC-MS/MSKonstantinos Boulias and Eric Lieberman Greer8. 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 Gackowski9. MS Analysis of DNA Modifications in Urinary/Body FluidsAleksandra Skalska, Agnieszka Siomek-Gorecka, Ryszard Olinski, and Rafal Rozalski10. Preparation of Internal Standards for 2D-UPLC-MS/MS Quantification of Non-Canonical DNA BasesMarta Starczak, Aleksandra Skalska, Rafal Rozalski, Ryszard Olinski, and Daniel Gackowski11. Detection of TET-Oxidized 5-Methylcytosine Bases by Capillary Gel ElectrophoresisRomualdas Vaisvila, Lise Hunault, and Lana SalehPart III: Assessing the Levels and Spatial Distribution of DNA Modifications Using Antibody-Based Approaches12. Immunochemical Detection of Modified Cytosine Species in Mammalian Preimplantation EmbryosTie-Bo Zeng and Piroska E. Szabo13. Immunochemical Detection of Modified Cytosine Species in Lampbrush ChromatinGarry T. Morgan14. Detection of Low-Abundance DNA Modifications Using Signal Amplification-Based ImmunocytochemistryAbdulkadir Abakir and Alexey Ruzov15. Immunohistochemical Detection of Modified Cytosine Bases in Rodent BrainMarcus D. Wallis and Rebecca C. Trueman16. Immunohistochemical Detection of 5-Hydroxymethylcytosine and 5-Carboxylcytosine in Sections of Zebrafish EmbryosPeter Jessop and Martin Gering17. Immunochemical Detection of Modified Species of Cytosine in Plant TissuesMarcos Viejo, Igor Yakovlev, and Carl Gunnar Fossdal18. Antigen Retrieval for Immunostaining of Modified Cytosine SpeciesSelcen Celik-Uzuner19. Computational Analysis of DNA Modifications in Confocal ImagesSeema Rajani, Christopher Gell, Abdulkadir Abakir, and Robert Markus20. Three-Dimensional Confocal Analysis of Chromosome Positioning Coupled with Immunofluorescence in Mouse Sperm NucleiAlexandre Champroux, Chantal Goubely, Joelle Henry-Berger, Joel R. Drevet, and Ayhan Kocer21. Analysis of 5-Hydroxymethyluracil Levels Using Flow CytometryLidia Gackowska, Anna Labejszo, and Daniel GackowskiPart IV: Mapping DNA Modifications22. Hairpin-Bisulfite PCRReinhard Stoeger23. Genome-Wide Mapping of DNA Methylation 5mC by Methylated DNA Immunoprecipitation (MeDIP)-SequencingMillissia Ben Maamar, Ingrid Sadler-Riggleman, Daniel Beck, and Michael K. Skinner24. Analysis of 5-Carboxylcytosine Distribution Using DNA ImmunoprecipitationAbdulkadir Abakir, Fahad Alenezi, and Alexey Ruzov25. High Resolution Analysis of 5-Hydroxymethylcytosine by TET-Assisted Bisulfite SequencingZhijun Huang, Yingying Meng, Piroska E. Szabo, Rahul M. Kohli, and Gerd P. Pfeifer26. Oxidative Bisulfite Sequencing: An Experimental and Computational ProtocolMarie De Borre and Miguel R. Branco27. 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. Kohli28. Single-Nucleotide-Resolution Sequencing of N6-MethyldeoxyadenosineWee Siong Sho GohPart V: Applications of Genome Targeting Methods in Epigenetics29. Design and Application of DNA Modification-Specific Transcription-Activator-Like EffectorsBenjamin Buchmuller, Alvaro Munoz-Lopez, Mario Giess, and Daniel Summerer30. Notes on Functional Modules in the Assembly of CRISPR/Cas9-Mediated Epigenetic ModifiersAlexander Kondrashov and Elena KarpovaPart VI: Analysis of DNA Modifications Sequencing Datasets31. Analyzing DNA-Immunoprecipitation Sequencing DataAntonio Lentini and Colm E. Nestor32. Bioinformatics Analysis of DNA Methylation through Bisulfite Sequencing DataFei Sang33. Unified Analysis of Multiple ChIP-Seq DatasetsGang Ma, Isaac A. Babarinde, Qiang Zhuang, and Andrew P. Hutchins34. Integrated Analysis of DNA Methylation, Hydroxymethylation, and Gene Expression Data Using ME-Class2Manoj K. Singh and John R. Edwards