title: Reader domain specificity and lysine demethylase-4 family function.
abstract: The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray analysis uncovers trimethyl-lysine histone-binding preferences among the closely related KDM4 double tudor domains (DTDs). KDM4A/B DTDs bind strongly to H3K23me3, a poorly understood histone modification recently shown to be enriched in meiotic chromatin of ciliates and nematodes. The 2.28 Å co-crystal structure of KDM4A-DTD in complex with H3K23me3 peptide reveals key intermolecular interactions for H3K23me3 recognition. Furthermore, analysis of the 2.56 Å KDM4B-DTD crystal structure pinpoints the underlying residues required for exclusive H3K23me3 specificity, an interaction supported by in vivo co-localization of KDM4B and H3K23me3 at heterochromatin in mammalian meiotic and newly postmeiotic spermatocytes. In vitro demethylation assays suggest H3K23me3 binding by KDM4B stimulates H3K36 demethylation. Together, these results provide a possible mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis.
authors.affiliation: Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.|Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA.
authors.forename: Zhangli
authors.initials: Z
authors.lastname: Su
authors.affiliation: Biosciences at Rice, Rice University, Houston, Texas 77005, USA.
authors.forename: Fengbin
authors.initials: F
authors.lastname: Wang
authors.affiliation: Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.|Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA.
authors.forename: Jin-Hee
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.|Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors.forename: Kimberly E
authors.initials: KE
authors.lastname: Stephens
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.|Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors.forename: Romeo
authors.initials: R
authors.lastname: Papazyan
authors.affiliation: Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA.
authors.forename: Ekaterina
authors.identifier: http://orcid.org/0000-0002-0194-4260
authors.initials: E
authors.lastname: Voronina
authors.affiliation: Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.|Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA.
authors.forename: Kimberly A
authors.initials: KA
authors.lastname: Krautkramer
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.|Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors.forename: Ana
authors.initials: A
authors.lastname: Raman
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.|Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Thorpe
authors.affiliation: Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.|Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA.
authors.forename: Melissa D
authors.initials: MD
authors.lastname: Boersma
authors.affiliation: Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.|Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA.
authors.forename: Vyacheslav I
authors.initials: VI
authors.lastname: Kuznetsov
authors.affiliation: Biosciences at Rice, Rice University, Houston, Texas 77005, USA.
authors.forename: Mitchell D
authors.initials: MD
authors.lastname: Miller
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.|Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors.forename: Sean D
authors.initials: SD
authors.lastname: Taverna
authors.affiliation: Biosciences at Rice, Rice University, Houston, Texas 77005, USA.|Department of Chemistry, Rice University, Houston, Texas 77005, USA.|Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.
authors.forename: George N
authors.initials: GN
authors.lastname: Phillips
authors.affiliation: Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.|Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Denu
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D018360:Crystallography, X-Ray; D006657:Histones / Q000378:metabolism*; D006801:Humans; D007527:Isoenzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D056484:Jumonji Domain-Containing Histone Demethylases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008239:Lysine / Q000378:metabolism*; D008297:Male; D008745:Methylation; D008810:Mice, Inbred C57BL; D008958:Models, Molecular; D000072417:Protein Domains; D011499:Protein Processing, Post-Translational; D017207:Rats, Sprague-Dawley
chemical_list: D006657:Histones; D007527:Isoenzymes; D056484:Jumonji Domain-Containing Histone Demethylases; C494424:KDM4A protein, human; D008239:Lysine