DNA modifications: methods and protocols
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...
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
New York, NY
Humana Press
2021
|
| Schriftenreihe: | Methods in molecular biology
2198 |
| Schlagworte: | |
| Zusammenfassung: | 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 |
| Beschreibung: | 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 |
| Beschreibung: | xvi, 495 Seiten Illustrationen, Diagramme 1150 grams |
| ISBN: | 9781071608753 |
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| 500 | |a 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. | ||
| 500 | |a - 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. | ||
| 500 | |a - 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. | ||
| 500 | |a - 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. | ||
| 500 | |a - 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. | ||
| 500 | |a - 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 | ||
| 520 | |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. 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 | ||
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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. </subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a"> - 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. </subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a"> - 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. </subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a"> - 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. </subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a"> - 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</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="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. 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| id | DE-604.BV046900133 |
| illustrated | Illustrated |
| index_date | 2024-07-03T15:24:05Z |
| indexdate | 2024-07-10T08:56:57Z |
| institution | BVB |
| isbn | 9781071608753 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-032309805 |
| oclc_num | 1198211483 |
| open_access_boolean | |
| owner | DE-29T DE-19 DE-BY-UBM |
| owner_facet | DE-29T DE-19 DE-BY-UBM |
| physical | xvi, 495 Seiten Illustrationen, Diagramme 1150 grams |
| publishDate | 2021 |
| publishDateSearch | 2021 |
| publishDateSort | 2021 |
| publisher | Humana Press |
| record_format | marc |
| series | Methods in molecular biology |
| series2 | Methods in molecular biology Springer protocols |
| spelling | DNA modifications methods and protocols edited by Alexey Ruzov (Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham, UK), Martin Gering ( School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK) New York, NY Humana Press 2021 xvi, 495 Seiten Illustrationen, Diagramme 1150 grams txt rdacontent n rdamedia nc rdacarrier Methods in molecular biology 2198 Springer protocols 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 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 bicssc bisacsh Biology—Technique Genetics Life sciences Nucleotidsequenz (DE-588)4297525-6 gnd rswk-swf Modifikation Biochemie (DE-588)4307844-8 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf Molekularbiologische Methode (DE-588)7650063-9 gnd rswk-swf Organismus (DE-588)4043831-4 gnd rswk-swf Allgemeines, Lexika Organismus (DE-588)4043831-4 s DNS (DE-588)4070512-2 s Nucleotidsequenz (DE-588)4297525-6 s Modifikation Biochemie (DE-588)4307844-8 s Molekularbiologische Methode (DE-588)7650063-9 s DE-604 Ruzov, Alexey Sonstige (DE-588)1218623411 oth Gering, Martin 1966- Sonstige (DE-588)172930405 oth Erscheint auch als Online-Ausgabe 978-1-0716-0876-0 Methods in molecular biology 2198 (DE-604)BV035362695 2198 |
| spellingShingle | DNA modifications methods and protocols Methods in molecular biology bicssc bisacsh Biology—Technique Genetics Life sciences Nucleotidsequenz (DE-588)4297525-6 gnd Modifikation Biochemie (DE-588)4307844-8 gnd DNS (DE-588)4070512-2 gnd Molekularbiologische Methode (DE-588)7650063-9 gnd Organismus (DE-588)4043831-4 gnd |
| subject_GND | (DE-588)4297525-6 (DE-588)4307844-8 (DE-588)4070512-2 (DE-588)7650063-9 (DE-588)4043831-4 |
| title | DNA modifications methods and protocols |
| title_auth | DNA modifications methods and protocols |
| title_exact_search | DNA modifications methods and protocols |
| title_exact_search_txtP | DNA modifications methods and protocols |
| title_full | DNA modifications methods and protocols edited by Alexey Ruzov (Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham, UK), Martin Gering ( School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK) |
| title_fullStr | DNA modifications methods and protocols edited by Alexey Ruzov (Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham, UK), Martin Gering ( School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK) |
| title_full_unstemmed | DNA modifications methods and protocols edited by Alexey Ruzov (Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham, UK), Martin Gering ( School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK) |
| title_short | DNA modifications |
| title_sort | dna modifications methods and protocols |
| title_sub | methods and protocols |
| topic | bicssc bisacsh Biology—Technique Genetics Life sciences Nucleotidsequenz (DE-588)4297525-6 gnd Modifikation Biochemie (DE-588)4307844-8 gnd DNS (DE-588)4070512-2 gnd Molekularbiologische Methode (DE-588)7650063-9 gnd Organismus (DE-588)4043831-4 gnd |
| topic_facet | bicssc bisacsh Biology—Technique Genetics Life sciences Nucleotidsequenz Modifikation Biochemie DNS Molekularbiologische Methode Organismus |
| volume_link | (DE-604)BV035362695 |
| work_keys_str_mv | AT ruzovalexey dnamodificationsmethodsandprotocols AT geringmartin dnamodificationsmethodsandprotocols |