Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp992
Gene Regulation, Chromatin and Epigenetics |
MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
1Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Ave, mail code NE50 and 2Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, 9500 Euclid Ave, mail code Q10, Cleveland, OH, 44195, USA
*To whom correspondence should be addressed. Tel: +1 216 444 0682; Fax; +1 216 636 0009; Email: tinga{at}ccf.org
Correspondence may also be addressed to David Serre. Email: serred{at}ccf.org.
Received September 9, 2009. Revised October 14, 2009. Accepted October 15, 2009.
DNA methylation is an epigenetic modification involved in both normal developmental processes and disease states through the modulation of gene expression and the maintenance of genomic organization. Conventional methods of DNA methylation analysis, such as bisulfite sequencing, methylation sensitive restriction enzyme digestion and array-based detection techniques, have major limitations that impede high-throughput genome-wide analysis. We describe a novel technique, MBD-isolated Genome Sequencing (MiGS), which combines precipitation of methylated DNA by recombinant methyl-CpG binding domain of MBD2 protein and sequencing of the isolated DNA by a massively parallel sequencer. We utilized MiGS to study three isogenic cancer cell lines with varying degrees of DNA methylation. We successfully detected previously known methylated regions in these cells and identified hundreds of novel methylated regions. This technique is highly specific and sensitive and can be applied to any biological settings to identify differentially methylated regions at the genomic scale.
The authors wish it to be known that, in their opinion, first and third author should be regarded as joint First Authors.