title: A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions.
abstract: Post-translational modifications of histones, such as acetylation and methylation, are differentially positioned in chromatin with respect to gene organization. For example, although histone H3 is often trimethylated on lysine 4 (H3K4me3) and acetylated on lysine 14 (H3K14ac) at active promoter regions, histone H3 lysine 36 trimethylation (H3K36me3) occurs throughout the open reading frames of transcriptionally active genes. The conserved yeast histone acetyltransferase complex, NuA3, specifically binds H3K4me3 through a plant homeodomain (PHD) finger in the Yng1 subunit, and subsequently catalyzes the acetylation of H3K14 through the histone acetyltransferase domain of Sas3, leading to transcription initiation at a subset of genes. We previously found that Ylr455w (Pdp3), an uncharacterized proline-tryptophan-tryptophan-proline (PWWP) domain-containing protein, copurifies with stable members of NuA3. Here, we employ mass-spectrometric analysis of affinity purified Pdp3, biophysical binding assays, and genetic analyses to classify NuA3 into two functionally distinct forms: NuA3a and NuA3b. Although NuA3a uses the PHD finger of Yng1 to interact with H3K4me3 at the 5'-end of open reading frames, NuA3b contains the unique member, Pdp3, which regulates an interaction between NuA3b and H3K36me3 at the transcribed regions of genes through its PWWP domain. We find that deletion of PDP3 decreases NuA3-directed transcription and results in growth defects when combined with transcription elongation mutants, suggesting NuA3b acts as a positive elongation factor. Finally, we determine that NuA3a, but not NuA3b, is synthetically lethal in combination with a deletion of the histone acetyltransferase GCN5, indicating NuA3b has a specialized role at coding regions that is independent of Gcn5 activity. Collectively, these studies define a new form of the NuA3 complex that associates with H3K36me3 to effect transcriptional elongation. MS data are available via ProteomeXchange with identifier PXD001156.
authors.affiliation: From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205;
authors.forename: Tonya M
authors.initials: TM
authors.lastname: Gilbert
authors.affiliation: ¶Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599;
authors.forename: Stephen L
authors.initials: SL
authors.lastname: McDaniel
authors.affiliation: ‖Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205;
authors.forename: Stephanie D
authors.initials: SD
authors.lastname: Byrum
authors.affiliation: From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205;
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Cades
authors.affiliation: From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205;
authors.forename: Blair C R
authors.initials: BC
authors.lastname: Dancy
authors.affiliation: **Department of Biophysics and Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205;
authors.forename: Herschel
authors.initials: H
authors.lastname: Wade
authors.affiliation: ‖Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205;
authors.forename: Alan J
authors.initials: AJ
authors.lastname: Tackett
authors.affiliation: ¶Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599; ‡‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599 staverna@jhmi.edu brian_strahl@med.unc.edu.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Strahl
authors.affiliation: From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; staverna@jhmi.edu brian_strahl@med.unc.edu.
authors.forename: Sean D
authors.initials: SD
authors.lastname: Taverna
mesh_terms: D000107:Acetylation; D000595:Amino Acid Sequence; D004926:Escherichia coli / Q000235:genetics; D051548:Histone Acetyltransferases / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000378:metabolism*; D013058:Mass Spectrometry; D008745:Methylation; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010441:Peptide Chain Elongation, Translational / Q000235:genetics / Q000502:physiology; D010957:Plasmids / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics / Q000502:physiology; D011499:Protein Processing, Post-Translational; D017434:Protein Structure, Tertiary; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D016415:Sequence Alignment
chemical_list: D006657:Histones; D029701:Saccharomyces cerevisiae Proteins; D051548:Histone Acetyltransferases; C526757:SAS3 protein, S cerevisiae; C459900:Yng1 protein, S cerevisiae
references.citation: Cell Rep. 2012 Jul 26;2(1):198-205
references.pmid: 22840409
references.citation: J Biol Chem. 2012 Feb 3;287(6):4386-93
references.pmid: 22184112
references.citation: Proc Natl Acad Sci U S A. 2004 May 11;101(19):7357-62
references.pmid: 15123803
references.citation: EMBO J. 2004 Oct 27;23(21):4243-52
references.pmid: 15457216
references.citation: PLoS Genet. 2012;8(5):e1002717
references.pmid: 22615581
references.citation: Mol Cell. 2013 Oct 24;52(2):255-63
references.pmid: 24055344
references.citation: J Biol Chem. 2001 Nov 23;276(47):43653-62
references.pmid: 11544250
references.citation: Cold Spring Harb Perspect Biol. 2009 Oct;1(4):a000224
references.pmid: 20066094
references.citation: Genetics. 2010 Jun;185(2):469-77
references.pmid: 20351216
references.citation: Genes Dev. 2003 Mar 1;17(5):654-63
references.pmid: 12629047
references.citation: Biochim Biophys Acta. 2009 Jan;1789(1):26-36
references.pmid: 18718879
references.citation: Cell. 2005 Nov 18;123(4):581-92
references.pmid: 16286007
references.citation: Nat Protoc. 2009;4(3):363-71
references.pmid: 19247286
references.citation: Curr Opin Genet Dev. 2007 Apr;17(2):94-9
references.pmid: 17317148
references.citation: Mol Cell Biol. 2003 Oct;23(19):7005-18
references.pmid: 12972617
references.citation: J Biol Chem. 2009 Nov 20;284(47):32914-31
references.pmid: 19759026
references.citation: Nature. 2010 Dec 23;468(7327):1050-1
references.pmid: 21179160
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9
references.pmid: 23203882
references.citation: Nature. 2014 Apr 10;508(7495):263-8
references.pmid: 24590075
references.citation: PLoS One. 2011;6(6):e18919
references.pmid: 21720545
references.citation: Nat Biotechnol. 2014 Mar;32(3):223-6
references.pmid: 24727771
references.citation: Nature. 2012 Sep 20;489(7416):452-5
references.pmid: 22914091
references.citation: Anal Chem. 2002 Oct 15;74(20):5383-92
references.pmid: 12403597
references.citation: Methods Enzymol. 1987;154:164-75
references.pmid: 3323810
references.citation: Mol Cell Proteomics. 2012 Dec;11(12):1682-9
references.pmid: 22949509
references.citation: Curr Opin Cell Biol. 2006 Jun;18(3):291-8
references.pmid: 16647254
references.citation: J Mol Biol. 2011 May 27;409(1):36-46
references.pmid: 21272588
references.citation: Mol Cell Biol. 2009 Sep;29(17):4852-63
references.pmid: 19581288
references.citation: Methods Enzymol. 2012;512:107-35
references.pmid: 22910205
references.citation: J Cell Biol. 2005 Apr 11;169(1):35-47
references.pmid: 15824130
references.citation: Genes Dev. 2013 Sep 15;27(18):2009-24
references.pmid: 24065767
references.citation: Int J Cancer. 2010 Nov 1;127(9):2088-94
references.pmid: 20131318
references.citation: Mol Cell. 2006 Dec 8;24(5):785-796
references.pmid: 17157260
references.citation: EMBO J. 2012 Aug 29;31(17):3564-74
references.pmid: 22863776
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D565-70
references.pmid: 22123736
references.citation: J Biol Chem. 1999 Feb 26;274(9):5895-900
references.pmid: 10026213
references.citation: Yeast. 2004 Aug;21(11):947-62
references.pmid: 15334558
references.citation: Mol Microbiol. 2001 Apr;40(2):422-32
references.pmid: 11309124
references.citation: Mol Cell. 2007 Jul 20;27(2):275-88
references.pmid: 17643376
references.citation: Science. 2007 May 18;316(5827):1050-4
references.pmid: 17510366
references.citation: PLoS One. 2013;8(2):e54896
references.pmid: 23437046
references.citation: J Biol Chem. 2009 Mar 20;284(12):7970-6
references.pmid: 19155214
references.citation: Curr Cancer Drug Targets. 2008 Jun;8(4):275-84
references.pmid: 18537551
references.citation: Protein Sci. 2009 Sep;18(9):1987-97
references.pmid: 19621382
references.citation: Cell. 2010 Sep 17;142(6):967-80
references.pmid: 20850016
references.citation: Mol Cell Biol. 2006 Apr;26(8):3018-28
references.pmid: 16581777
references.citation: Mol Cell Biol. 2008 Aug;28(16):4915-26
references.pmid: 18541663
references.citation: Development. 2008 Jun;135(11):1935-46
references.pmid: 18469222
references.citation: J Biol Chem. 2002 Mar 8;277(10):7989-95
references.pmid: 11773077
references.citation: J Biol Chem. 2003 Mar 14;278(11):8897-903
references.pmid: 12511561
references.citation: PLoS One. 2009 Jun 12;4(6):e5882
references.pmid: 19521516
references.citation: J Biol Chem. 2002 Dec 20;277(51):49383-8
references.pmid: 12381723
references.citation: Nat Struct Mol Biol. 2010 May;17(5):617-9
references.pmid: 20400950
references.citation: Methods. 1998 Aug;15(4):315-21
references.pmid: 9740719
references.citation: PLoS One. 2009;4(3):e4886
references.pmid: 19295910
references.citation: Nature. 2006 Mar 30;440(7084):637-43
references.pmid: 16554755
references.citation: Genes Dev. 2001 Dec 1;15(23):3144-54
references.pmid: 11731478
references.citation: Mol Cell Biol. 2002 Mar;22(5):1577-88
references.pmid: 11839823
references.citation: J Biol Chem. 2005 Jan 21;280(3):1817-25
references.pmid: 15516689
references.citation: Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11325-30
references.pmid: 20534568
references.citation: Mol Cell Biol. 2008 Nov;28(22):6828-43
references.pmid: 18794358
references.citation: J Biol Chem. 1991 Apr 15;266(11):7025-9
references.pmid: 2016313
references.citation: Trends Biochem Sci. 2003 Feb;28(2):69-74
references.pmid: 12575993
references.citation: Genes Dev. 2001 Dec 15;15(24):3286-95
references.pmid: 11751634
references.citation: Nucleic Acids Res. 2013 Nov;41(20):e195
references.pmid: 24030711
references.citation: Mol Cell. 2005 Dec 22;20(6):971-8
references.pmid: 16364921
references.citation: Nucleic Acids Res. 2011 Aug;39(15):6369-79
references.pmid: 21515633
references.citation: Nat Struct Mol Biol. 2012 Sep;19(9):884-92
references.pmid: 22922743
references.citation: EMBO J. 2001 Feb 1;20(3):552-61
references.pmid: 11157761
references.citation: J Biol Chem. 2010 Aug 20;285(34):26114-20
references.pmid: 20547484
references.citation: Nature. 2013 Oct 24;502(7472):480-8
references.pmid: 24153301
references.citation: Oncogene. 2007 Aug 13;26(37):5395-407
references.pmid: 17694081
references.citation: Mutat Res. 2007 May 1;618(1-2):130-4
references.pmid: 17346757
references.citation: Nat Biotechnol. 2012 Feb 08;30(2):135-7
references.pmid: 22318026
references.citation: Mol Cell Biol. 2012 Sep;32(17):3479-85
references.pmid: 22751925
references.citation: Nucleic Acids Res. 2003 May 15;31(10):2475-82
references.pmid: 12736296
references.citation: Mol Cell Biol. 2009 Dec;29(24):6473-87
references.pmid: 19822662
references.citation: Genes Dev. 2007 Jun 1;21(11):1422-30
references.pmid: 17545470
references.citation: Mol Cell Biol. 2002 Mar;22(5):1298-306
references.pmid: 11839797
references.citation: Nat Struct Mol Biol. 2012 Nov;19(11):1155-60
references.pmid: 23022729
references.citation: Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11622-7
references.pmid: 12186975
references.citation: Eukaryot Cell. 2005 Aug;4(8):1446-54
references.pmid: 16087749
references.citation: Nat Struct Mol Biol. 2007 Nov;14(11):1025-1040
references.pmid: 17984965
references.citation: Nature. 2000 Jan 6;403(6765):41-5
references.pmid: 10638745
references.citation: Biochem Biophys Res Commun. 2005 Jul 1;332(2):398-403
references.pmid: 15896708
references.citation: Mol Cell Biol. 2003 Jun;23(12):4207-18
references.pmid: 12773564
references.citation: Mol Cell. 2006 Jan 6;21(1):51-64
references.pmid: 16387653
references.citation: Anal Chem. 2003 Sep 1;75(17):4646-58
references.pmid: 14632076
references.citation: Mol Cell. 2007 Jan 12;25(1):31-42
references.pmid: 17218269
references.citation: Nat Struct Mol Biol. 2009 Dec;16(12):1272-8
references.pmid: 19935686
references.citation: Biochem J. 2012 Mar 15;442(3):527-38
references.pmid: 22150589
references.citation: Crit Rev Biochem Mol Biol. 2010 Dec;45(6):488-505
references.pmid: 20923397
references.citation: J Biol Chem. 2008 Feb 22;283(8):5058-68
references.pmid: 18089575
references.citation: Mol Cell Biol. 2005 Apr;25(8):3305-16
references.pmid: 15798214
references.citation: EMBO J. 1998 Jun 1;17(11):3155-67
references.pmid: 9606197
references.citation: Cell. 2005 Nov 18;123(4):593-605
references.pmid: 16286008
references.citation: Epigenetics. 2013 Jan;8(1):10-5
references.pmid: 23257840
references.citation: J Proteome Res. 2005 Sep-Oct;4(5):1752-6
references.pmid: 16212429
references.citation: Trends Genet. 2012 Jun;28(6):285-94
references.pmid: 22465610
references.citation: Genes Dev. 2000 May 15;14(10):1196-208
references.pmid: 10817755
references.citation: BMC Genomics. 2009 Nov 24;10:554
references.pmid: 19930675
references.citation: EMBO J. 2011 Jun 17;30(14):2829-42
references.pmid: 21685874
references.citation: Cell. 2005 Aug 26;122(4):517-27
references.pmid: 16122420
references.citation: J Biol Chem. 2008 Dec 26;283(52):36504-12
references.pmid: 18984594
references.citation: Nat Rev Mol Cell Biol. 2012 Jan 23;13(2):115-26
references.pmid: 22266761
references.citation: Mol Cell Biol. 2006 Apr;26(8):3029-38
references.pmid: 16581778
references.citation: Structure. 2008 Nov 12;16(11):1740-50
references.pmid: 18818090
references.citation: Mol Cell Biol. 2006 Nov;26(21):7871-9
references.pmid: 16923967
references.citation: Mol Cell Biol. 2002 Jul;22(14):5047-53
references.pmid: 12077334
references.citation: Epigenetics. 2014 Feb;9(2):186-93
references.pmid: 24169304