title: High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology.
abstract: Methyl-CpG binding domain protein sequencing (MBD-seq) is widely used to survey DNA methylation patterns. However, the optimal experimental parameters for MBD-seq remain unclear and the data analysis remains challenging. In this study, we generated high depth MBD-seq data in MCF-7 cell and developed a bi-asymmetric-Laplace model (BALM) to perform data analysis. We found that optimal efficiency of MBD-seq experiments was achieved by sequencing ∼100 million unique mapped tags from a combination of 500 mM and 1000 mM salt concentration elution in MCF-7 cells. Clonal bisulfite sequencing results showed that the methylation status of each CpG dinucleotides in the tested regions was accurately detected with high resolution using the proposed model. These results demonstrated the combination of MBD-seq and BALM could serve as a useful tool to investigate DNA methylome due to its low cost, high specificity, efficiency and resolution.
authors.affiliation: Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America.
authors.forename: Xun
authors.initials: X
authors.lastname: Lan
authors.forename: Christopher
authors.initials: C
authors.lastname: Adams
authors.forename: Mark
authors.initials: M
authors.lastname: Landers
authors.forename: Miroslav
authors.initials: M
authors.lastname: Dudas
authors.forename: Daniel
authors.initials: D
authors.lastname: Krissinger
authors.forename: George
authors.initials: G
authors.lastname: Marnellos
authors.forename: Russell
authors.initials: R
authors.lastname: Bonneville
authors.forename: Maoxiong
authors.initials: M
authors.lastname: Xu
authors.forename: Junbai
authors.initials: J
authors.lastname: Wang
authors.forename: Tim H-M
authors.initials: TH
authors.lastname: Huang
authors.forename: Gavin
authors.initials: G
authors.lastname: Meredith
authors.forename: Victor X
authors.initials: VX
authors.lastname: Jin
mesh_terms: D002460:Cell Line; D019175:DNA Methylation / Q000235:genetics*; D015226:Dinucleoside Phosphates / Q000378:metabolism*; D006801:Humans; D008954:Models, Biological; D008967:Molecular Biology / Q000379:methods*
chemical_list: D015226:Dinucleoside Phosphates; C015772:CpG dinucleotide