Epigenetics Methods

Section 1: Overview
1. An Overview of Epigenetics Methods

Section 2: DNA Methylation Methods: Gene- or Locus-specific Methylation Analyses
2. Principles of Bisulfite Conversion of DNA and Methylation-specific PCR (MSP) in Biological Research
3. Multiplex Methylation Specific Droplet Digital PCR (MS-ddPCR) for Detection and of Rare Methylated Alleles

Section 3: DNA Methylation Methods: Global DNA Methylation and Methylomic Analyses
4. Methods for Detection of DNA Methylation in Transposable Elements
5. The Illumina Infinium Methylation Assay for Genome-wide Methylation Analyses
6. Methylated DNA Immunoprecipitation Sequencing: Methodological Principles and Applications
7. Multiplex Analyses Using Methylation Sensitive Restriction Enzyme coupled qPCR and NGS
8. Advances in Whole Genome Methylomic Sequencing

Section 4: DNA Methylation Methods: Additional Technologies
9. Analyzing DNA Methyltransferase Enzymatic Activity: Basic Methods and Applications
10. Technologies and Applications for the Assessment of 5-Hydroxymethylcytosine

Section 5: Histone Modification Methods
11. The Chromatin Immunoprecipitation (ChIP) Assay and ChIP-qPCR
12. CUT&RUN and CUT&Tag for histone modification and transcription factor binding analyses
13. Deep Sequencing for Histone Modifications Employing ChIP-seq Analyses
14. ChIP in Series: Sequential ChIP
15. The ChIP-exo Method to Study DNA-protein interactions and Chromatin Organization at Near-Nucleotide Resolution
16. ATAC-seq Method Applied to Embryonic Germ Cells and Neural Stem Cells from Mouse: Practical
17. Combinatorial ChIP and Bisulfite Sequencing (BisChIP-seq)

Section 6: Epigenetic Methods for Evaluating Chromatin Higher Order
18. 3D DNA FISH for Analyses of Nuclear Chromatin Architecture

Section 7: Enzyme Analyses of Histone Modifications
19. Assessment of Histone-Modifying Enzymes Involved in Epigenetic Gene Regulation

Section 8: Assessment of Non-Coding RNA as an Epigenetic Modulator
20. Detection and Quantification of MicroRNAs (miRNAs) and High Throughput miRNAs Profiling
21. RIP-seq in Epigenetic Analyses
22. Chromatin Isolation by RNA Purification (ChIRP) and Its Applications

Section 9: Additional Epigenetics Methods
23. Single-Cell Epigenomics: Methods and Translation
24. CRISPR/Cas9 Technologies in Epigenetics Research
25. Epigenome-Wide Association Study (EWAS) Methods and Applications
26. Systems Biology Methods to Study the Epigenome and Metabolic- epigenetic Interactions
27. Forensic Epigenetics Methods and Applications

Section 10: Future Directions in Epigenetics Methodology
28. Advances in Epigenetic Techniques to Study Development and Diseases