title: Combined Interactions of Plant Homeodomain and Chromodomain Regulate NuA4 Activity at DNA Double-Strand Breaks.
abstract: DNA double-strand breaks (DSBs) represent one of the most threatening lesions to the integrity of genomes. In yeast Saccharomyces cerevisiae, NuA4, a histone acetylation complex, is recruited to DSBs, wherein it acetylates histones H2A and H4, presumably relaxing the chromatin and allowing access to repair proteins. Two subunits of NuA4, Yng2 and Eaf3, can interact in vitro with methylated H3K4 and H3K36 via their plant homeodomain (PHD) and chromodomain. However, the roles of the two domains and how they interact in a combinatorial fashion are still poorly characterized. In this study, we generated mutations in the PHD and chromodomain that disrupt their interaction with methylated H3K4 and H3K36. We demonstrate that the combined mutations in both the PHD and chromodomain impair the NuA4 recruitment, reduce H4K12 acetylation at the DSB site, and confer sensitivity to bleomycin that induces DSBs. In addition, the double mutant cells are defective in DSB repair as judged by Southern blot and exhibit prolonged activation of phospho-S129 of H2A. Cells harboring the H3K4R, H3K4R, K36R, or set1Δ set2Δ mutant that disrupts H3K4 and H3K36 methylation also show very similar phenotypes to the PHD and chromodomain double mutant. Our results suggest that multivalent interactions between the PHD, chromodomain, and methylated H3K4 and H3K36 act in a combinatorial manner to recruit NuA4 and regulate the NuA4 activity at the DSB site.
authors.affiliation: Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Wen-Pin
authors.initials: WP
authors.lastname: Su
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Sen-Huei
authors.initials: SH
authors.lastname: Hsu
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Li-Chiao
authors.initials: LC
authors.lastname: Chia
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Jui-Yang
authors.initials: JY
authors.lastname: Lin
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Song-Bin
authors.initials: SB
authors.lastname: Chang
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Zong-da
authors.initials: ZD
authors.lastname: Jiang
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Yi-Ju
authors.initials: YJ
authors.lastname: Lin
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Min-Yu
authors.initials: MY
authors.lastname: Shih
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Yi-Cheng
authors.initials: YC
authors.lastname: Chen
authors.affiliation: Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.
authors.forename: Mau-Sun
authors.initials: MS
authors.lastname: Chang
authors.affiliation: Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Wen-Bin
authors.initials: WB
authors.lastname: Yang
authors.affiliation: Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Jan-Jong
authors.initials: JJ
authors.lastname: Hung
authors.affiliation: Department of Electrical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Po-Cheng
authors.initials: PC
authors.lastname: Hung
authors.affiliation: Department of Electrical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Wei-Sheng
authors.initials: WS
authors.lastname: Wu
authors.affiliation: Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Kyungjae
authors.initials: K
authors.lastname: Myung
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan liawh@mail.ncku.edu.tw.
authors.forename: Hungjiun
authors.identifier: http://orcid.org/0000-0002-3481-709X
authors.initials: H
authors.lastname: Liaw
mesh_terms: D000107:Acetylation; D000123:Acetyltransferases / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D001761:Bleomycin / Q000494:pharmacology; D002843:Chromatin / Q000378:metabolism; D053903:DNA Breaks, Double-Stranded; D004271:DNA, Fungal / Q000378:metabolism*; D025141:Drug Resistance, Fungal / Q000235:genetics; D051548:Histone Acetyltransferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000378:metabolism; D018398:Homeodomain Proteins / Q000378:metabolism*; D008745:Methylation; D009154:Mutation; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D002843:Chromatin; D004271:DNA, Fungal; D006657:Histones; D018398:Homeodomain Proteins; D029701:Saccharomyces cerevisiae Proteins; D001761:Bleomycin; D000123:Acetyltransferases; C428131:Eaf3 protein, S cerevisiae; C469780:Yng2 protein, S cerevisiae; C496551:Esa1 protein, S cerevisiae; D051548:Histone Acetyltransferases; C504740:NuA4 protein, S cerevisiae
keywords: DSB repair; NuA4; Saccharomyces cerevisiae; histone modification; multivalent interaction