title: Methyl-CpG/MBD2 Interaction Requires Minimum Separation and Exhibits Minimal Sequence Specificity.
abstract: Determining the pattern of methylation at CpG dinucleotides in a cell remains an essential component of epigenetic profiling. The correlations among methylation, gene expression, and accompanying disease have just begun to be explored. Many experiments for sensing methylation use a relatively inexpensive, high-throughput approach with a methyl-binding domain (MBD) protein that preferentially binds to methylated CpGs. Here, we characterize the cooperativity and sequence specificity of MBD2-DNA binding in a pulldown experiment revealing three potential biases in such experiments. The first is caused by steric clashes between two MBD2 proteins at mCpGs separated by 2 bp or less, which suggests that simultaneous binding at these sites is inhibited. This is confirmed by comparing input versus pulldown high-throughput sequencing data on M.SssI-treated samples, from which we also find that pulldown efficiency sharply increases for DNA fragments with four or more mCpGs. Analysis of these two data sets was again employed to investigate MBD2's sequence preferences surrounding a methylated CpG (mCpG). In comparing the distributions of bases at positions with respect to an mCpG, statistically significant preferences for certain bases were found, although the corresponding biases in pulldown efficiency were all <5%. While this suggests that mCpG sequence context can mostly be ignored in MBD2 binding, the statistical certainty exhibited by our high-throughput approach bodes well for future applications.
authors.affiliation: Department of Physics, The Ohio State University, Columbus, Ohio.
authors.forename: Blythe
authors.initials: B
authors.lastname: Moreland
authors.affiliation: Department of Physics, The Ohio State University, Columbus, Ohio.
authors.forename: Kenji
authors.initials: K
authors.lastname: Oman
authors.affiliation: Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, Ohio.
authors.forename: John
authors.initials: J
authors.lastname: Curfman
authors.affiliation: Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, Ohio.
authors.forename: Pearlly
authors.initials: P
authors.lastname: Yan
authors.affiliation: Department of Physics, The Ohio State University, Columbus, Ohio; Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, Ohio; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Center for RNA Biology, The Ohio State University, Columbus, Ohio. Electronic address: bundschuh@mps.ohio-state.edu.
authors.forename: Ralf
authors.initials: R
authors.lastname: Bundschuh
mesh_terms: D001483:Base Sequence; D018899:CpG Islands / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008745:Methylation; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D013379:Substrate Specificity
chemical_list: D004268:DNA-Binding Proteins; C115368:MBD2 protein; D004247:DNA