Epigenetics Methods, Second Edition offers an extensive overview of the tools that enhance translational epigenetics studies. This edition includes updated and revised chapters, along with newly added topics such as MALDI-TOF-MS for analyzing DNA methylation and the RIP assay for lncRNA binding. Specialists provide step-by-step guidance on methods used to study various epigenetic mechanisms. The book covers both fundamental and advanced techniques, making it an essential resource for researchers in this dynamic field. In addition to DNA methylation and histone modification techniques, the book also explores chromatin evaluation, enzyme analyses, and non-coding RNAs as epigenetic modulators.
New chapters discuss recent advancements like single-cell epigenomics, epigenetic editing, and computational epigenetics. The volume addresses reproducibility issues and offers consensus-driven methods to unify approaches across experiments and labs. This edition is a vital reference for understanding and employing cutting-edge epigenetics methods.
1. Title of Book - p. i 2. Cover image - p. i 3. Title page - p. ii 4. Table of Contents - p. iii 5. Copyright - p. iv 6. Contributors - p. xv 7. Preface - p. xxi 8. Section 1. Overview - p. 1 9. Chapter One. An overview of epigenetics methods - p. 3 10. Section 2. DNA methylation methods: Gene- or locus-specific methylation analyses - p. 15 11. Chapter Two. Principles of bisulfite conversion of DNA and methylation-specific PCR in biological research - p. 17 12. Chapter Three. Multiplex methylation specific droplet digital PCR (MS-ddPCR) for detection and quantification of rare methylated alleles - p. 33 13. Section 3. DNA methylation methods: Global DNA methylation and methylomic analyses - p. 51 14. Chapter Four. Methods for detection of DNA methylation in transposable elements - p. 53 15. Chapter Five. The Illumina Infinium methylation assay for genome-wide methylation analyses - p. 85 16. Chapter Six. Methylated DNA immunoprecipitation sequencing: Methodological principles and applications - p. 107 17. Chapter Seven. Multiplex analyses using methylation sensitive restriction enzyme coupled qPCR and NGS - p. 141 18. Chapter Eight. Advances in whole genome methylomic sequencing - p. 177 19. Section 4. DNA methylation methods: Additional technologies - p. 207 20. Chapter Nine. Analyzing DNA methyltransferase enzymatic activity: Basic methods and applications - p. 209 21. Chapter Ten. Technologies and applications for the assessment of 5-hydroxymethylcytosine - p. 239 22. Section 5. Histone modification methods - p. 259 23. Chapter Eleven. The chromatin immunoprecipitation (ChIP) assay and ChIP-qPCR - p. 261 24. Chapter Twelve. CUT&RUN and CUT&Tag for histone modification and transcription factor binding analyses - p. 279 25. Chapter thirteen. Deep sequencing for histone modifications using ChIP-seq analysis - p. 297 26. Chapter Fourteen. ChIP in series: Sequential ChIP - p. 325 27. Chapter Fifteen. The ChIP-exo method to study DNA-protein interactions and chromatin organization at near-nucleotide resolution - p. 355 28. Chapter Sixteen. ATAC-seq method applied to embryonic germ cells and neural stem cells from mouse: Practical tips and modifications - p. 371 29. Chapter seventeen. Combinatorial ChIP and bisulfite sequencing (BisChIP-seq) - p. 393 30. Section 6. Epigenetic methods for evaluating chromatin higher order - p. 407 31. Chapter Eighteen. 3D DNA FISH for analyses of nuclear chromatin architecture - p. 409 32. Section 7. Enzyme analyses of histone modifications - p. 433 33. Chapter Nineteen. Assessment of histone-modifying enzymes involved in epigenetic gene regulation - p. 435 34. Section 8. Assessment of noncoding RNA as an epigenetic modulator - p. 471 35. Chapter Twenty. Detection and quantification of MicroRNAs (miRNAs) and high-throughput miRNAs profiling - p. 473 36. Chapter Twenty One. RIP-seq in epigenetic analyses - p. 489 37. Chapter Twenty Two. Chromatin isolation by RNA purification (ChIRP) and its applications - p. 509 38. Section 9. Additional epigenetics methods - p. 529 39. Chapter Twenty Three. Single-cell epigenomics: Methods and translation - p. 531 40. Chapter Twenty Four. CRISPR/Cas technologies in epigenetics research - p. 549 41. Chapter twenty five. Epigenome-wide association study (EWAS) methods and applications - p. 591 42. Chapter Twenty six. Systems biology methods to study the epigenome and metabolic-epigenetic interactions - p. 617 43. Chapter Twenty Seven. Forensic epigenetics methods and applications - p. 663 44. Section 10. Future directions in epigenetics methodology - p. 687 45. Chapter Twenty Eight. Advances in epigenetic techniques to study development and diseases - p. 689 46. Index - p. 713
Epigenetics Methods, Second Edition offers an extensive overview of the tools that enhance translational epigenetics studies. This edition includes updated and revised chapters, along with newly added topics such as MALDI-TOF-MS for analyzing DNA methylation and the RIP assay for lncRNA binding. Specialists provide step-by-step guidance on methods used to study various epigenetic mechanisms. The book covers both fundamental and advanced techniques, making it an essential resource for researchers in this dynamic field. In addition to DNA methylation and histone modification techniques, the book also explores chromatin evaluation, enzyme analyses, and non-coding RNAs as epigenetic modulators.
New chapters discuss recent advancements like single-cell epigenomics, epigenetic editing, and computational epigenetics. The volume addresses reproducibility issues and offers consensus-driven methods to unify approaches across experiments and labs. This edition is a vital reference for understanding and employing cutting-edge epigenetics methods.
1. Title of Book - p. i 2. Cover image - p. i 3. Title page - p. ii 4. Table of Contents - p. iii 5. Copyright - p. iv 6. Contributors - p. xv 7. Preface - p. xxi 8. Section 1. Overview - p. 1 9. Chapter One. An overview of epigenetics methods - p. 3 10. Section 2. DNA methylation methods: Gene- or locus-specific methylation analyses - p. 15 11. Chapter Two. Principles of bisulfite conversion of DNA and methylation-specific PCR in biological research - p. 17 12. Chapter Three. Multiplex methylation specific droplet digital PCR (MS-ddPCR) for detection and quantification of rare methylated alleles - p. 33 13. Section 3. DNA methylation methods: Global DNA methylation and methylomic analyses - p. 51 14. Chapter Four. Methods for detection of DNA methylation in transposable elements - p. 53 15. Chapter Five. The Illumina Infinium methylation assay for genome-wide methylation analyses - p. 85 16. Chapter Six. Methylated DNA immunoprecipitation sequencing: Methodological principles and applications - p. 107 17. Chapter Seven. Multiplex analyses using methylation sensitive restriction enzyme coupled qPCR and NGS - p. 141 18. Chapter Eight. Advances in whole genome methylomic sequencing - p. 177 19. Section 4. DNA methylation methods: Additional technologies - p. 207 20. Chapter Nine. Analyzing DNA methyltransferase enzymatic activity: Basic methods and applications - p. 209 21. Chapter Ten. Technologies and applications for the assessment of 5-hydroxymethylcytosine - p. 239 22. Section 5. Histone modification methods - p. 259 23. Chapter Eleven. The chromatin immunoprecipitation (ChIP) assay and ChIP-qPCR - p. 261 24. Chapter Twelve. CUT&RUN and CUT&Tag for histone modification and transcription factor binding analyses - p. 279 25. Chapter thirteen. Deep sequencing for histone modifications using ChIP-seq analysis - p. 297 26. Chapter Fourteen. ChIP in series: Sequential ChIP - p. 325 27. Chapter Fifteen. The ChIP-exo method to study DNA-protein interactions and chromatin organization at near-nucleotide resolution - p. 355 28. Chapter Sixteen. ATAC-seq method applied to embryonic germ cells and neural stem cells from mouse: Practical tips and modifications - p. 371 29. Chapter seventeen. Combinatorial ChIP and bisulfite sequencing (BisChIP-seq) - p. 393 30. Section 6. Epigenetic methods for evaluating chromatin higher order - p. 407 31. Chapter Eighteen. 3D DNA FISH for analyses of nuclear chromatin architecture - p. 409 32. Section 7. Enzyme analyses of histone modifications - p. 433 33. Chapter Nineteen. Assessment of histone-modifying enzymes involved in epigenetic gene regulation - p. 435 34. Section 8. Assessment of noncoding RNA as an epigenetic modulator - p. 471 35. Chapter Twenty. Detection and quantification of MicroRNAs (miRNAs) and high-throughput miRNAs profiling - p. 473 36. Chapter Twenty One. RIP-seq in epigenetic analyses - p. 489 37. Chapter Twenty Two. Chromatin isolation by RNA purification (ChIRP) and its applications - p. 509 38. Section 9. Additional epigenetics methods - p. 529 39. Chapter Twenty Three. Single-cell epigenomics: Methods and translation - p. 531 40. Chapter Twenty Four. CRISPR/Cas technologies in epigenetics research - p. 549 41. Chapter twenty five. Epigenome-wide association study (EWAS) methods and applications - p. 591 42. Chapter Twenty six. Systems biology methods to study the epigenome and metabolic-epigenetic interactions - p. 617 43. Chapter Twenty Seven. Forensic epigenetics methods and applications - p. 663 44. Section 10. Future directions in epigenetics methodology - p. 687 45. Chapter Twenty Eight. Advances in epigenetic techniques to study development and diseases - p. 689 46. Index - p. 713
