Methods to analyze DNA methylation, DNA demethylation, and their functional effects are critical to epigenetics researchers. Methylation profiles of epigenome are used for disease identification and for research and therapeutic development. Analysis can be gene-specific or global depending on downstream applications (1).
Downstream methylation detection methods include end-point PCR, real-time PCR, primer extension, single-stranded conformational polymorphism assays, blotting, microarray analysis and sequencing. Choosing which method(s) to use largely depends on the experimental sample size and the goals of the experiments.
- Tao Zuo et al. 2009, Epigenomics 1(2) 331-345. PMID: 20526417
DNA Methylation Analysis includes these areas of focus:
FAQs for DNA Methylation Analysis
- Does the T4-BGT show any site preference?
- Do I need to do extra purification steps for a mammalian DNA prep in order to use it in a glucosylation reaction?
- How do I know if the glucosylation of 5-hmC in my DNA is complete?
- How much control DNA should I use in my qPCR?
- What is the shelf life of the reagents supplied?
- What products does NEB offer for the study of Epigenetics?
Protocols for DNA Methylation Analysis
Application Notes DNA Methylation Analysis
Epigenetics - Expanding on Genomic Foundations
The Epigenetics brochure provides information on these unique solutions to study DNA and histone modifications. NEB offers a suite of validated products for epigenetics research.
- EpiMark® Methylated DNA Enrichment Kit Troubleshooting Guide
Other Tools & Resources
- Hughes J.R., Roberts N., McGowan S., Hay D., Giannoulatou E., Lynch M., De Gobbi M., Taylor S., Gibbons R., Higgs D.R. 2014. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment Nat Genet. 46 (2), PubMedID: 24413732, DOI: doi:10.1038/ng.2871
- Sexton T, Kurukuti S, Mitchell JA, Umlauf D, Nagano T, Fraser P 2012. Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip Nat Protoc. 7(7), PubMedID: 22722369, DOI: 10.1038/nprot.2012.071
Publications related to DNA Methylation Analysis
Methods of DNA Methylation Analysis
- Bisulfite conversion, which provides single nucleotide, high resolution data for whole genomes or single locus methylation studies.
- Differential enzymatic cleavage, which uses methylation, or dually 5-mC and 5-hmC dependent enzymes, paired with non-sensitive isoschizomers to asses DNA methylation or DNA hydroxymethylation.
- High-Performance Liquid Chromatography (HPLC)
- Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry(MALDI-TOF MS)
- Methylated DNA-ELISA
- Affinity-based methods, which use methylated DNA binding proteins or antibodies for enrichment.
- Enzymatic DNA methyltransferase assay
If all cells are created from the same genetic material, why are there so many different cell types? Listen to Sriharsa Pradhan, Senior Scientist, RNA Biology at NEB, as he describes how DNA is methylated and how this affects the path of reading the DNA code the same way an obstruction would derail a train off its tracks.