title: Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36.
abstract: The PHD finger motif is a signature chromatin-associated motif that is found throughout eukaryotic proteomes. Here we have determined the histone methyl-lysine binding activity of the PHD fingers present within the Saccharomyces cerevisiae proteome. We provide evidence on the genomic scale that PHD fingers constitute a general class of effector modules for histone H3 trimethylated at lysine 4 (H3K4me3) and histone H3 trimethylated at lysine 36 (H3K36me3). Structural modeling of PHD fingers demonstrates a conserved mechanism for recognizing the trimethyl moiety and provides insight into the molecular basis of affinity for the different methyl-histone ligands. Together, our study suggests that a common function for PHD fingers is to transduce methyl-lysine events and sheds light on how a single histone modification can be linked to multiple biological outcomes.
authors.affiliation: Department of Biological Sciences, Stanford University, Stanford, California 94305, USA.
authors.forename: Xiaobing
authors.initials: X
authors.lastname: Shi
authors.forename: Ioulia
authors.initials: I
authors.lastname: Kachirskaia
authors.forename: Kay L
authors.initials: KL
authors.lastname: Walter
authors.forename: Jen-Hao A
authors.initials: JH
authors.lastname: Kuo
authors.forename: Aimee
authors.initials: A
authors.lastname: Lake
authors.forename: Foteini
authors.initials: F
authors.lastname: Davrazou
authors.forename: Steve M
authors.initials: SM
authors.lastname: Chan
authors.forename: David G E
authors.initials: DG
authors.lastname: Martin
authors.forename: Ian M
authors.initials: IM
authors.lastname: Fingerman
authors.forename: Scott D
authors.initials: SD
authors.lastname: Briggs
authors.forename: LeAnn
authors.initials: L
authors.lastname: Howe
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Utz
authors.forename: Tatiana G
authors.initials: TG
authors.lastname: Kutateladze
authors.forename: Alexey A
authors.initials: AA
authors.lastname: Lugovskoy
authors.forename: Mark T
authors.initials: MT
authors.lastname: Bedford
authors.forename: Or
authors.initials: O
authors.lastname: Gozani
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D004268:DNA-Binding Proteins; D006657:Histones / Q000378:metabolism*; D018398:Homeodomain Proteins / Q000737:chemistry / Q000378:metabolism; D008239:Lysine; D008745:Methylation; D008969:Molecular Sequence Data; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D020543:Proteome; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D006657:Histones; D018398:Homeodomain Proteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D008239:Lysine