title: Methylation specific targeting of a chromatin remodeling complex from sponges to humans.
abstract: DNA cytosine methylation and methyl-cytosine binding domain (MBD) containing proteins are found throughout all vertebrate species studied to date. However, both the presence of DNA methylation and pattern of methylation varies among invertebrate species. Invertebrates generally have only a single MBD protein, MBD2/3, that does not always contain appropriate residues for selectively binding methylated DNA. Therefore, we sought to determine whether sponges, one of the most ancient extant metazoan lineages, possess an MBD2/3 capable of recognizing methylated DNA and recruiting the associated nucleosome remodeling and deacetylase (NuRD) complex. We find that Ephydatia muelleri has genes for each of the NuRD core components including an EmMBD2/3 that selectively binds methylated DNA. NMR analyses reveal a remarkably conserved binding mode, showing almost identical chemical shift changes between binding to methylated and unmethylated CpG dinucleotides. In addition, we find that EmMBD2/3 and EmGATAD2A/B proteins form a coiled-coil interaction known to be critical for the formation of NuRD. Finally, we show that knockdown of EmMBD2/3 expression disrupts normal cellular architecture and development of E. muelleri. These data support a model in which the MBD2/3 methylation-dependent functional role emerged with the earliest multicellular organisms and has been maintained to varying degrees across animal evolution.
authors.affiliation: Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Cramer
authors.affiliation: Department of Biology, University of Richmond, Richmond, VA, USA.
authors.forename: Deborah
authors.initials: D
authors.lastname: Pohlmann
authors.affiliation: Department of Biology, University of Richmond, Richmond, VA, USA.
authors.forename: Fernando
authors.initials: F
authors.lastname: Gomez
authors.affiliation: Department of Biology, University of Richmond, Richmond, VA, USA.
authors.forename: Leslie
authors.initials: L
authors.lastname: Mark
authors.affiliation: Department of Biology, University of Richmond, Richmond, VA, USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Kornegay
authors.affiliation: Department of Biology, University of Richmond, Richmond, VA, USA.
authors.forename: Chelsea
authors.initials: C
authors.lastname: Hall
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
authors.forename: Edhriz
authors.initials: E
authors.lastname: Siraliev-Perez
authors.affiliation: Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
authors.forename: Ninad M
authors.initials: NM
authors.lastname: Walavalkar
authors.affiliation: Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
authors.forename: M Jeannette
authors.initials: MJ
authors.lastname: Sperlazza
authors.affiliation: Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Bilinovich
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
authors.forename: Jeremy W
authors.initials: JW
authors.lastname: Prokop
authors.affiliation: Department of Biology, University of Richmond, Richmond, VA, USA.
authors.forename: April L
authors.initials: AL
authors.lastname: Hill
authors.affiliation: Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Williams
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D042002:Chromatin Assembly and Disassembly; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D055785:Gene Knockdown Techniques; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010641:Phenotype; D011161:Porifera / Q000235:genetics* / Q000378:metabolism; D011487:Protein Conformation
chemical_list: D004268:DNA-Binding Proteins; C115368:MBD2 protein; D004247:DNA