Methyl-CpG Binding Domain (MBD)_Based Capture and Sequencing / Capture of Methylated DNA Using the Methyl-CpG Binding Domain MBD domain of MeCP2 / Methyl-CpG Binding Domain_Isolated Genome Sequencing

MBDCap (Rauch et al., 2008) (Rauch et al., 2009) and MethylCap (Bock et al., 2010) (Brinkman et al., 2010) enrich methylated DNA by affinity purification. These methods are particularly suitable to investigate regional blocks of hypermethylation. The term MiGS is easily confused with the common term MIGS (minimum information about a genome sequence), and is rarely used.

In these methods, gDNA is first sonicated and incubated with tagged MBD proteins that can bind methylated cytosines. Next, the protein-DNA complex is precipitated with antibody-conjugated beads that are specific to the protein tag. The DNA is purified and used to prepare a sequencing library. Deep sequencing provides greater genome coverage, representing the majority of MBD-bound methylated DNA.


  • Interrogates regional blocks of hypermethylation
  • Compared to HM450K arrays, MBDCap-seq regional coverage of shores (77% vs 28%), enhancers (12% vs 2%), and insulators (11% vs 1%) is much greater (Stirzaker et al., 2015)
  • MBDCap-Seq from formalin-fixed paraffin-embedded (FFPE) tissues provides equivalent methylation data to fresh-frozen DNA
  • MDB proteins can discriminate between 5mC and 5hmC (Yong et al., 2016)


  • Base-pair resolution is lower (~150 bp), as opposed to single-base resolution with other methods
  • Biased toward hypermethylated regions


Illumina Library prep and Array Kit Selector


Soto J., Rodriguez-Antolin C., Vallespin E., de Castro Carpeno J. and Ibanez de Caceres I. The impact of next-generation sequencing on the DNA methylation-based translational cancer research. Transl Res. 2016;169:1-18 e11

Tang J., Fang F., Miller D. F., Pilrose J. M., Matei D., et al. Global DNA methylation profiling technologies and the ovarian cancer methylome. Methods Mol Biol. 2015;1238:653-675

Yong W. S., Hsu F. M. and Chen P. Y. Profiling genome-wide DNA methylation. Epigenetics Chromatin. 2016;9:26


Boers A., Wang R., van Leeuwen R. W., et al. Discovery of new methylation markers to improve screening for cervical intraepithelial neoplasia grade 2/3. Clin Epigenetics. 2016;8:29

Stirzaker C., Zotenko E., Song J. Z., et al. Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Nat Commun. 2015;6:5899

Wang Y., Jadhav R. R., Liu J., et al. Roles of Distal and Genic Methylation in the Development of Prostate Tumorigenesis Revealed by Genome-wide DNA Methylation Analysis. Sci Rep. 2016;6:22051

Clausen M. J., Melchers L. J., Mastik M. F., et al. Identification and validation of WISP1 as an epigenetic regulator of metastasis in oral squamous cell carcinoma. Genes Chromosomes Cancer. 2016;55:45-59

Zhang X. L., Wu J., Wang J., et al. Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells. Genome Biol. 2016;17:162

Locke W. J., Zotenko E., Stirzaker C., et al. Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis. Clin Epigenetics. 2015;7:52