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Epigenetic Services

MeDIP-Sequencing (MeDIP-Seq)

determine genome-wide DNA methylation patterns

The reliable identification of differential DNA methylation is important for researchers interested in biomarker identification, as well as for those trying to understand the basis of disease, drug mechanism of action or environmental influences on epigenetics. To help speed research in these areas, Active Motif now offers MeDIP-Seq as an end-to-end, genome-wide epigenetic service to identify differentially methylated regions.

The MeDIP-Seq Service includes:

Customers submit purified DNA, frozen tissues or cell pellets, then we:

  1. Prepare the sample.
  2. Perform MeDIP with a 5-mC mAb.
  3. Amplify the enriched DNA sample.
  4. Perform Next-Gen sequencing.
  5. Analyze the data and deliver it to the customer.

To learn more, please give us a call or send us an Epigenetic Services Information Request. You can also download Active Motif’s Epigenetic Services Profile.

 
Name Cat No. Price  
MethylPath™ MeDIP-Seq 25025 Request Quote
MethylPath™ MeDIP-qPCR 25024 Request Quote
Sequencing of Input / Control DNA 25046 Request Quote

How does MeDIP-Seq work?

In MeDIP-Seq, a highly specific antibody that recognizes 5-methylcytosine is used to immunoprecipitate sonicated genomic DNA, resulting in the enrichment of genomic regions that are methylated. Because 5-methylcytosine antibody binds only to methylated cytosines in the context of single-stranded DNA, the DNA must be denatured prior to immunoprecipitation. As a result of denaturation the enriched DNA can not be processed for Next-Gen sequencing using the typical sequencing library generation protocols, as these require adaptor ligation to double-stranded DNA. This problem is circumvented by ligating the Next-Gen sequencing adaptors to genomic DNA prior to the immunoprecipitation. Following MeDIP, the enriched regions can be directly amplified with Next-Gen sequencing compatible primers. Unique alignment of the sequence tags across the genome reveals the regions of DNA methylation.

MeDIP-Seq data generated by Active Motif Epigenetic Services correlate well with that in published, publicly available data set
Results from Active Motif’s MeDIP-Seq Service correlate well with published MeDIP results.

This image shows a 30 Kb region on chromosome 13. The top panel is data from a published, publicly available data set while the bottom was produced by Active Motif’s MeDIP-Seq Service. Overlaid gray peaks show CpG density across the region.

MeDIP-Seq advantages

Several methodologies exist that can detect DNA methylation on a genome-wide scale. Whole genome bisulfite sequencing is the most comprehensive, providing single base resolution across the entire genome. However, it requires sequencing of the entire genome, which is extremely expensive. Reduced Representation Bisulfite Sequencing (RRBS) also yields single base resolution, but it only interrogates 10% of all CpGs and it is more heavily biased toward CpG-rich regions than any other technique. This is not necessarily an advantage as most CpG islands are unmethylated, and because there is growing interest and focus on regions with lower CpG density. MeDIP-Seq coverage is not as biased toward high CpG density and in theory can interrogate all regions across the genome. The expanded genomic coverage of MeDIP-Seq compared to RRBS increases the likelihood of identifying differentially methylated regions in multi-sample studies.

MeDIP-Seq data generated by Active Motif Epigenetic Services compared to CpG density and to Reduced Representation Bisulfite Sequencing (RRBS)
MeDIP-Seq data compared to CpG density and RRBS.

MeDIP-Seq was performed using 2 µg of DNA from human PBMCs. Methylation peaks were mapped across the genome and the image is zoomed in to look at the ADCY1 gene. The middle panel shows good correlation of MeDIP signal (purple bars) with CpG density (overlaid gray peaks) indicating that MeDIP covers most CpG sites across the ADCY1 gene. RRBS data is shown at the top as blue bars; the coverage is limited to only a few regions.