Genome-wide DNA Methylation Profiling
The Epigenomics Core offers different assays measuring Genome-wide DNA Methylation. This sequence-based technology provides information on DNA methylation status across the genome at different levels of resolution:
Whole-genome bisulfite sequencing (WGBS): whole-genome base-pair resolution quantification of DNA methylation following bisulfite conversion of unmodified cytosines (considered the gold standard)
ERRBS (Enhanced Reduced Representation Bisulfite Sequencing): Quantitative base-pair measurement of cytosine methylation at ~2M CpGs (species dependent) genome-wide located at promoters, CpG islands and shores, and intergenic regulatory regions
Illumina MethylationEPIC BeadChip v2: we offer this service in partnership with the UM Advanced Genomics Core. We perform DNA quality control and bisulfite conversion on the samples, then bring them to AGC for hybridization and scanning. We also perform QC on the data generated before transfer back to the investigator.
meDIP-Seq: Investigators may still request meDIP-seq (Antibody-based method for identification of mC-enriched areas across the genome). The core will purchase the kits required for the project.
**NEW** We now offer NEB’s EM-Seq: this is a whole-genome base-pair resolution technique that uses an enzyme for cytosine deamination instead of bisulfite conversion. DNA must be of good quality and with no contaminants for best results. Contact Managing Director for more information.
** NEW** Twist Biosciences Human Methylome Panel: This is a Capture Panel targeting 3.98M CpG across the human genome. Up to 8 libraries can be pooled before Capture. Contact Managing Director for more information.
Targeted (locus-specific) DNA Methylation
Targeted DNA methylation allows for the locus-specific detection of cytosine methylation by bisulfite-sequencing. The Targeted DNA Methylation services at the Epigenomics Core include:
- Primer design consultation
- Bisulfite conversion of DNA and PCR amplification of target sequences (Enzymatic deamination can also be used, depending on the project.)
- Amplicon Bisulfite-Sequencing: amplicons generated for each sample are converted in NGS libraries and sequenced on a MiSeq nano flow cell.
- Pyrosequencing (Note: this technology will be discontinued by the end of 2023.)
- Support with data analysis
Hydroxymethylation: Genome-wide and Target Specific
5-Hydroxymethylcytosine (5hmC) is part of the DNA demethylation process and mediated by the TET enzymes. DNA demethylation has been associated with activation of gene expression. The Epigenomics Core is actively testing new assays to measure 5hmC. At this time, these are the assays that can be used:
- OxBS + BS: this is the only currently validated for 5hmC. Note that this assay can be performed for both NGS sequencing and for MethylationEPIC arrays. We use Tecan’s OxBS kit for either assays. Measurement of 5hmC with this assay requires 2 reactions that are performed side by side: reaction 1 is the usual bisulfite conversion protocol (measures 5mC + 5 hmC); Reaction 2 is performs oxidation of 5hmC in the presence of potassium perruthenate before bisulfite conversion (5mC only). Comparison of the readout of both reactions is needed to impute 5hmC levels, either after NGS sequencing of the libraries, or EPIC array hybridization.
- hmeDIP-seq: Antibody-based method for the identification of 5-hmC-enriched areas across the genome
- hmeDIP: Antibody-based method for the identification of 5-hmC enrichment at specific loci