title: DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells.
abstract: Cytosine methylation is an epigenetic and regulatory mark that functions in part through recruitment of chromatin remodeling complexes containing methyl-CpG binding domain (MBD) proteins. Two MBD proteins, Mbd2 and Mbd3, were previously shown to bind methylated or hydroxymethylated DNA, respectively; however, both of these findings have been disputed. Here, we investigated this controversy using experimental approaches and re-analysis of published data and find no evidence for methylation-independent functions of Mbd2 or Mbd3. We show that chromatin localization of Mbd2 and Mbd3 is highly overlapping and, unexpectedly, we find Mbd2 and Mbd3 are interdependent for chromatin association. Further investigation reveals that both proteins are required for normal levels of cytosine methylation and hydroxymethylation in murine embryonic stem cells. Furthermore, Mbd2 and Mbd3 regulate overlapping sets of genes that are also regulated by DNA methylation/hydroxymethylation factors. These findings reveal an interdependent regulatory mechanism mediated by the DNA methylation machinery and its readers.
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Hainer
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.
authors.forename: Kurtis N
authors.initials: KN
authors.lastname: McCannell
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.
authors.forename: Ly-Sha
authors.initials: LS
authors.lastname: Ee
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.|Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States.|Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States.
authors.forename: Lihua J
authors.initials: LJ
authors.lastname: Zhu
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.
authors.forename: Oliver J
authors.initials: OJ
authors.lastname: Rando
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.|Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States.
authors.forename: Thomas G
authors.identifier: 0000-0002-0353-7466
authors.initials: TG
authors.lastname: Fazzio
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism; D000818:Animals; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D002874:Chromosome Mapping; D018899:CpG Islands; D000076123:DNA (Cytosine-5-)-Methyltransferase 1 / Q000172:deficiency / Q000235:genetics; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000172:deficiency / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D016678:Genome; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D061251:Primary Cell Culture; D011518:Proto-Oncogene Proteins / Q000172:deficiency / Q000235:genetics; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; C489326:Mbd2 protein, mouse; C492013:Mbd3 protein, mouse; D011518:Proto-Oncogene Proteins; C540839:TET1 protein, mouse; D014157:Transcription Factors; D044503:5-Methylcytosine; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; C000619381:Dnmt1 protein, mouse
keywords: DNA hydroxymethylation; DNA methylation; NuRD; chromatin; chromosomes; developmental biology; embryonic stem cells; genes; mouse; nucleosome; stem cells