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Widespread regulation of gene expression in the Drosophila genome by the histone acetyltransferase dTip60

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Abstract

The MYST histone acetyltransferase (HAT) dTip60 is part of a multimeric protein complex that unites both HAT and chromatin remodeling activities. Here, we sought to gain insight into the biological functions of dTip60. Strong ubiquitous dTip60 knock-down in flies was lethal, whereas knock-down in the wing imaginal disk led to developmental defects in the wing. dTip60 localized to the nucleus in early embryos and was present in a large number of interbands on polytene chromosomes. Genome-wide expression analysis upon depletion of dTip60 in cell culture showed that it regulated a large number of genes in Drosophila, among which those with chromatin-related functions were highly enriched. Surprisingly, a significant portion of these genes were upregulated upon dTip60 loss, indicating that dTip60 has repressive as well as activating functions. dTip60 protein was directly located at promoter regions of a subset of repressed genes, suggesting a direct role in gene repression. Comparison of the gene expression signature of dTip60 downregulation with that of histone deacetylase inhibition with trichostatin A revealed a significant correlation, suggesting that the dTip60 complex recruits an HDAC-containing complex to regulate gene expression in the Drosophila genome.

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Abbreviations

TSA:

trichostatin A

HAT:

histone acetyltransferase

HDAC:

histone deacetylase

References

  • Ai W, Zheng H, Yang X, Liu Y, Wang TC (2007) Tip60 functions as a potential corepressor of KLF4 in regulation of HDC promoter activity. Nucleic Acids Res 35:6137–6149

    Article  CAS  PubMed  Google Scholar 

  • Akhtar A, Zink D, Becker PB (2000) Chromodomains are protein–RNA interaction modules. Nature 407:405–409

    Article  CAS  PubMed  Google Scholar 

  • Bauer A, Chauvet S, Huber O, Usseglio F, Rothbacher U, Aragnol D, Kemler R, Pradel J (2000) Pontin52 and reptin52 function as antagonistic regulators of beta-catenin signalling activity. Embo J 19:6121–6130

    Article  CAS  PubMed  Google Scholar 

  • Beissbarth T, Speed TP (2004) GOstat: find statistically overrepresented gene ontologies within a group of genes. Bioinformatics 20:1464–1465

    Article  CAS  PubMed  Google Scholar 

  • Bellosta P, Hulf T, Balla Diop S, Usseglio F, Pradel J, Aragnol D, Gallant P (2005) Myc interacts genetically with Tip48/Reptin and Tip49/Pontin to control growth and proliferation during Drosophila development. Proc Natl Acad Sci U S A 102:11799–11804

    Article  CAS  PubMed  Google Scholar 

  • Brand AH, Perrimon N (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118:401–415

    CAS  PubMed  Google Scholar 

  • Carrozza MJ, Utley RT, Workman JL, Cote J (2003) The diverse functions of histone acetyltransferase complexes. Trends Genet 19:321–329

    Article  CAS  PubMed  Google Scholar 

  • Ceol CJ, Horvitz HR (2004) A new class of C. elegans synMuv genes implicates a Tip60/NuA4-like HAT complex as a negative regulator of Ras signaling. Dev Cell 6:563–576

    Article  CAS  PubMed  Google Scholar 

  • Diop SB, Bertaux K, Vasanthi D, Sarkeshik A, Goirand B, Aragnol D, Tolwinski NS, Cole MD, Pradel J, Yates JR 3rd et al (2008) Reptin and Pontin function antagonistically with PcG and TrxG complexes to mediate Hox gene control. EMBO Rep 9:260–266

    Article  CAS  PubMed  Google Scholar 

  • Doyon Y, Selleck W, Lane WS, Tan S, Cote J (2004) Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Mol Cell Biol 24:1884–1896

    Article  CAS  PubMed  Google Scholar 

  • Ebert A, Lein S, Schotta G, Reuter G (2006) Histone modification and the control of heterochromatic gene silencing in Drosophila. Chromosome Res 14:377–392

    Article  CAS  PubMed  Google Scholar 

  • Eggert H, Gortchakov A, Saumweber H (2004) Identification of the Drosophila interband-specific protein Z4 as a DNA-binding zinc-finger protein determining chromosomal structure. J Cell Sci 117:4253–4264

    Article  CAS  PubMed  Google Scholar 

  • Ehrenhofer-Murray AE (2004) Chromatin dynamics at DNA replication, transcription and repair. Eur J Biochem 271:2335–2349

    Article  CAS  PubMed  Google Scholar 

  • Ehrenhofer-Murray AE, Rivier DH, Rine J (1997) The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function. Genetics 145:923–934

    CAS  PubMed  Google Scholar 

  • Foglietti C, Filocamo G, Cundari E, De Rinaldis E, Lahm A, Cortese R, Steinkuhler C (2006) Dissecting the biological functions of Drosophila histone deacetylases by RNA interference and transcriptional profiling. J Biol Chem 281:17968–17976

    Article  CAS  PubMed  Google Scholar 

  • Frank SR, Parisi T, Taubert S, Fernandez P, Fuchs M, Chan HM, Livingston DM, Amati B (2003) MYC recruits the TIP60 histone acetyltransferase complex to chromatin. EMBO Rep 4:575–580

    Article  CAS  PubMed  Google Scholar 

  • Gallant P (2007) Control of transcription by Pontin and Reptin. Trends Cell Biol 17:187–192

    Article  CAS  PubMed  Google Scholar 

  • Gaughan L, Brady ME, Cook S, Neal DE, Robson CN (2001) Tip60 is a co-activator specific for class I nuclear hormone receptors. J Biol Chem 276:46841–46848

    Article  CAS  PubMed  Google Scholar 

  • Gause M, Eissenberg JC, Macrae AF, Dorsett M, Misulovin Z, Dorsett D (2006) Nipped-A, the Tra1/TRRAP subunit of the Drosophila SAGA and Tip60 complexes, has multiple roles in Notch signaling during wing development. Mol Cell Biol 26:2347–2359

    Article  CAS  PubMed  Google Scholar 

  • Gavaravarapu S, Kamine J (2000) Tip60 inhibits activation of CREB protein by protein kinase A. Biochem Biophys Res Commun 269:758–766

    Article  CAS  PubMed  Google Scholar 

  • Gorrini C, Squatrito M, Luise C, Syed N, Perna D, Wark L, Martinato F, Sardella D, Verrecchia A, Bennett S et al (2007) Tip60 is a haplo-insufficient tumour suppressor required for an oncogene-induced DNA damage response. Nature 448:1063–1067

    Article  CAS  PubMed  Google Scholar 

  • Gortchakov AA, Eggert H, Gan M, Mattow J, Zhimulev IF, Saumweber H (2005) Chriz, a chromodomain protein specific for the interbands of Drosophila melanogaster polytene chromosomes. Chromosoma 114:54–66

    Article  CAS  PubMed  Google Scholar 

  • Grienenberger A, Miotto B, Sagnier T, Cavalli G, Schramke V, Geli V, Mariol MC, Berenger H, Graba Y, Pradel J (2002) The MYST domain acetyltransferase Chameau functions in epigenetic mechanisms of transcriptional repression. Curr Biol 12:762–766

    Article  CAS  PubMed  Google Scholar 

  • Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293–296

    Article  CAS  PubMed  Google Scholar 

  • Hayward P, Brennan K, Sanders P, Balayo T, DasGupta R, Perrimon N, Martinez Arias A (2005) Notch modulates Wnt signalling by associating with Armadillo/beta-catenin and regulating its transcriptional activity. Development 132:1819–1830

    Article  CAS  PubMed  Google Scholar 

  • Ikura T, Ogryzko VV, Grigoriev M, Groisman R, Wang J, Horikoshi M, Scully R, Qin J, Nakatani Y (2000) Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102:463–473

    Article  CAS  PubMed  Google Scholar 

  • Kamine J, Elangovan B, Subramanian T, Coleman D, Chinnadurai G (1996) Identification of a cellular protein that specifically interacts with the essential cysteine region of the HIV-1 Tat transactivator. Virology 216:357–366

    Article  CAS  PubMed  Google Scholar 

  • Kesper DA, Stute C, Buttgereit D, Kreiskother N, Vishnu S, Fischbach KF, Renkawitz-Pohl R (2007) Myoblast fusion in Drosophila melanogaster is mediated through a fusion-restricted myogenic-adhesive structure (FuRMAS). Dev Dyn 236:404–415

    Article  CAS  PubMed  Google Scholar 

  • Kim MY, Ann EJ, Kim JY, Mo JS, Park JH, Kim SY, Seo MS, Park HS (2007) Tip60 histone acetyltransferase acts as a negative regulator of Notch1 signaling by means of acetylation. Mol Cell Biol 27:6506–6519

    Article  CAS  PubMed  Google Scholar 

  • Kimura A, Umehara T, Horikoshi M (2002) Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing. Nat Genet 32:370–377

    Article  PubMed  Google Scholar 

  • Kind J, Vaquerizas JM, Gebhardt P, Gentzel M, Luscombe NM, Bertone P, Akhtar A (2008) Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell 133:813–828

    Article  CAS  PubMed  Google Scholar 

  • Kramer JM, Staveley BE (2003) GAL4 causes developmental defects and apoptosis when expressed in the developing eye of Drosophila melanogaster. Genet Mol Res 2:43–47

    CAS  PubMed  Google Scholar 

  • Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates JR 3rd, Abmayr SM, Washburn MP, Workman JL (2004) Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 306:2084–2087

    Article  CAS  PubMed  Google Scholar 

  • Legube G, Linares LK, Tyteca S, Caron C, Scheffner M, Chevillard-Briet M, Trouche D (2004) Role of the histone acetyl transferase Tip60 in the p53 pathway. J Biol Chem 279:44825–44833

    Article  CAS  PubMed  Google Scholar 

  • Meijsing SH, Ehrenhofer-Murray AE (2001) The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae. Genes Dev 15:3169–3182

    Article  CAS  PubMed  Google Scholar 

  • Mendjan S, Akhtar A (2007) The right dose for every sex. Chromosoma 116:95–106

    Article  PubMed  Google Scholar 

  • Miotto B, Sagnier T, Berenger H, Bohmann D, Pradel J, Graba Y (2006) Chameau HAT and DRpd3 HDAC function as antagonistic cofactors of JNK/AP-1-dependent transcription during Drosophila metamorphosis. Genes Dev 20:101–112

    Article  CAS  PubMed  Google Scholar 

  • Mottus R, Sobel RE, Grigliatti TA (2000) Mutational analysis of a histone deacetylase in Drosophila melanogaster: missense mutations suppress gene silencing associated with position effect variegation. Genetics 154:657–668

    CAS  PubMed  Google Scholar 

  • Muller H, Fogeron ML, Lehmann V, Lehrach H, Lange BM (2006) A centrosome-independent role for gamma-TuRC proteins in the spindle assembly checkpoint. Science 314:654–657

    Article  PubMed  Google Scholar 

  • Negeri D, Eggert H, Gienapp R, Saumweber H (2002) Inducible RNA interference uncovers the Drosophila protein Bx42 as an essential nuclear cofactor involved in Notch signal transduction. Mech Dev 117:151–162

    Article  CAS  PubMed  Google Scholar 

  • Ni JQ, Markstein M, Binari R, Pfeiffer B, Liu LP, Villalta C, Booker M, Perkins L, Perrimon N (2008) Vector and parameters for targeted transgenic RNA interference in Drosophila melanogaster. Nat Methods 5:49–51

    Article  CAS  PubMed  Google Scholar 

  • Patel JH, Du Y, Ard PG, Phillips C, Carella B, Chen CJ, Rakowski C, Chatterjee C, Lieberman PM, Lane WS et al (2004) The c-MYC oncoprotein is a substrate of the acetyltransferases hGCN5/PCAF and TIP60. Mol Cell Biol 24:10826–10834

    Article  CAS  PubMed  Google Scholar 

  • Qi D, Jin H, Lilja T, Mannervik M (2006) Drosophila Reptin and other TIP60 complex components promote generation of silent chromatin. Genetics 174:241–251

    Article  CAS  PubMed  Google Scholar 

  • R Development Core Team (2008) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna

    Google Scholar 

  • Reifsnyder C, Lowell J, Clarke A, Pillus L (1996) Yeast SAS silencing genes and human genes associated with AML and HIV-1 Tat interactions are homologous with acetyltransferases. Nat Genet 14:42–49

    Article  CAS  PubMed  Google Scholar 

  • Robertson HM, Preston CR, Phillis RW, Johnson-Schlitz DM, Benz WK, Engels WR (1988) A stable genomic source of P element transposase in Drosophila melanogaster. Genetics 118:461–470

    CAS  PubMed  Google Scholar 

  • Sanjuan R, Marin I (2001) Tracing the origin of the compensasome: evolutionary history of DEAH helicase and MYST acetyltransferase gene families. Mol Biol Evol 18:330–343

    CAS  PubMed  Google Scholar 

  • Sapountzi V, Logan IR, Robson CN (2006) Cellular functions of TIP60. Int J Biochem Cell Biol 38:1496–1509

    Article  CAS  PubMed  Google Scholar 

  • Shia WJ, Li B, Workman JL (2006) SAS-mediated acetylation of histone H4 Lys 16 is required for H2A.Z incorporation at subtelomeric regions in Saccharomyces cerevisiae. Genes Dev 20:2507–2512

    Article  CAS  PubMed  Google Scholar 

  • Squatrito M, Gorrini C, Amati B (2006) Tip60 in DNA damage response and growth control: many tricks in one HAT. Trends Cell Biol 16:433–442

    Article  CAS  PubMed  Google Scholar 

  • Suka N, Luo K, Grunstein M (2002) Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin. Nat Genet 32:378–383

    Article  CAS  PubMed  Google Scholar 

  • Swaminathan J, Baxter EM, Corces VG (2005) The role of histone H2Av variant replacement and histone H4 acetylation in the establishment of Drosophila heterochromatin. Genes Dev 19:65–76

    Article  CAS  PubMed  Google Scholar 

  • Sykes SM, Mellert HS, Holbert MA, Li K, Marmorstein R, Lane WS, McMahon SB (2006) Acetylation of the p53 DNA-binding domain regulates apoptosis induction. Mol Cell 24:841–851

    Article  CAS  PubMed  Google Scholar 

  • Tang Y, Luo J, Zhang W, Gu W (2006) Tip60-dependent acetylation of p53 modulates the decision between cell-cycle arrest and apoptosis. Mol Cell 24:827–839

    Article  CAS  PubMed  Google Scholar 

  • Taubert S, Gorrini C, Frank SR, Parisi T, Fuchs M, Chan HM, Livingston DM, Amati B (2004) E2F-dependent histone acetylation and recruitment of the Tip60 acetyltransferase complex to chromatin in late G1. Mol Cell Biol 24:4546–4556

    Article  CAS  PubMed  Google Scholar 

  • Tautz D, Pfeifle C (1989) A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchback. Chromosoma 98:81–85

    Article  CAS  PubMed  Google Scholar 

  • Utley RT, Cote J (2003) The MYST family of histone acetyltransferases. Curr Top Microbiol Immunol 274:203–236

    CAS  PubMed  Google Scholar 

  • Wu CH, Yamaguchi Y, Benjamin LR, Horvat-Gordon M, Washinsky J, Enerly E, Larsson J, Lambertsson A, Handa H, Gilmour D (2003) NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev 17:1402–1414

    Article  CAS  PubMed  Google Scholar 

  • Xiao H, Chung J, Kao HY, Yang YC (2003) Tip60 is a co-repressor for STAT3. J Biol Chem 278:11197–11204

    Article  CAS  PubMed  Google Scholar 

  • Zhu X, Singh N, Donnelly C, Boimel P, Elefant F (2007) The cloning and characterization of the histone acetyltransferase human homolog Dmel\TIP60 in Drosophila melanogaster: Dmel\TIP60 is essential for multicellular development. Genetics 175:1229–1240

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We are indebted to Peter B. Becker and Gunter Reuter for reagents. Bodo M. H. Lange and Hannah Müller are gratefully acknowledged for advice concerning RNAi in Drosophila cultured cells. Lothar Vassen is thanked for advice on the analysis of microarray experiments. We further thank Irina Passow, Renate Gienap, and Christiane Vole for excellent technical assistance and the Ehrenhofer-Murray lab for many helpful discussions. This project was funded by the Max-Planck-Society and the University of Duisburg-Essen.

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Authors and Affiliations

  1. Abteilung für Genetik, Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, Universitätsstraße 5, 45117, Essen, Germany

    Corinna Schirling, Christiane Heseding, Franziska Heise & Ann E. Ehrenhofer-Murray

  2. Abteilung für Entwicklungsbiologie, Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, Essen, Germany

    Dörthe Kesper & Andrea Vortkamp

  3. Abteilung für Bioinformatik, Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, Essen, Germany

    Daniel Hoffmann

  4. Institut für Biologie-Genetik, Freie Universität Berlin, Berlin, Germany

    Ansgar Klebes

  5. Institut für Zellbiologie, Universitätsklinikum, Essen, Germany

    Ludger Klein-Hitpass

  6. Abteilung Zytogenetik, Institut für Biologie, Humboldt Universität Berlin, Berlin, Germany

    Harald Saumweber

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  1. Corinna Schirling
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  3. Franziska Heise
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Correspondence to Ann E. Ehrenhofer-Murray.

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Communicated by C. Lehner

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Supplementary Fig. 1

Ubiquitous expression of dTip60 RNA during embryogenesis. Lateral views of embryos hybridized with digoxigenin-labeled RNA probes of dTip60 in antisense (a, b) and, as a control, in sense (c, d) orientation. Enrichment of staining at mesoderm and endoderm is likely to be due to the thickness of tissue in these regions (JPEG 85 kb)

High resolution (TIFF 7291 kb)

Supplementary Fig. 2

Comparison of the anti-dTip60 antibody with the respective preimmune serum. a, c DAPI staining, b staining with anti-dTip60, d staining with preimmune serum. Slides are from the same batch, and no image processing was used (JPEG 49 kb)

High resolution (TIFF 911 kb)

Supplementary Fig. 3

Position of the dsRNA fragments used for dTip60-RNAi knock-down in SL2 cells, position of the dTip60 mRNA fragment measured by RT-PCR, and position of the fragments used for the UAS-dTip60-RNAi construct. The positions are indicated relative to the cDNA of dTip60, which is derived from the cDNA clone LD31064. Horizontal bars indicate the intron–exon borders. (JPEG 86 kb)

High resolution (TIFF 7159 kb)

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Schirling, C., Heseding, C., Heise, F. et al. Widespread regulation of gene expression in the Drosophila genome by the histone acetyltransferase dTip60. Chromosoma 119, 99–113 (2010). https://doi.org/10.1007/s00412-009-0247-z

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