Chromosoma

, Volume 119, Issue 1, pp 99–113

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

  • Corinna Schirling
  • Christiane Heseding
  • Franziska Heise
  • Dörthe Kesper
  • Ansgar Klebes
  • Ludger Klein-Hitpass
  • Andrea Vortkamp
  • Daniel Hoffmann
  • Harald Saumweber
  • Ann E. Ehrenhofer-Murray
Research Article

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.

Abbreviations

TSA

trichostatin A

HAT

histone acetyltransferase

HDAC

histone deacetylase

Supplementary material

412_2009_247_Fig1_ESM.jpg (86 kb)
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)

412_2009_247_Fig1_ESM.tif (7.1 mb)
High resolution (TIFF 7291 kb)
412_2009_247_Fig2_ESM.jpg (50 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)

412_2009_247_Fig2_ESM.tif (911 kb)
High resolution (TIFF 911 kb)
412_2009_247_Fig3_ESM.jpg (86 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)

412_2009_247_Fig3_ESM.tif (7 mb)
High resolution (TIFF 7159 kb)

References

  1. 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 35:6137–6149CrossRefPubMedGoogle Scholar
  2. Akhtar A, Zink D, Becker PB (2000) Chromodomains are protein–RNA interaction modules. Nature 407:405–409CrossRefPubMedGoogle Scholar
  3. 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 19:6121–6130CrossRefPubMedGoogle Scholar
  4. Beissbarth T, Speed TP (2004) GOstat: find statistically overrepresented gene ontologies within a group of genes. Bioinformatics 20:1464–1465CrossRefPubMedGoogle Scholar
  5. 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 102:11799–11804CrossRefPubMedGoogle Scholar
  6. Brand AH, Perrimon N (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118:401–415PubMedGoogle Scholar
  7. Carrozza MJ, Utley RT, Workman JL, Cote J (2003) The diverse functions of histone acetyltransferase complexes. Trends Genet 19:321–329CrossRefPubMedGoogle Scholar
  8. 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 6:563–576CrossRefPubMedGoogle Scholar
  9. 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 9:260–266CrossRefPubMedGoogle Scholar
  10. 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 24:1884–1896CrossRefPubMedGoogle Scholar
  11. Ebert A, Lein S, Schotta G, Reuter G (2006) Histone modification and the control of heterochromatic gene silencing in Drosophila. Chromosome Res 14:377–392CrossRefPubMedGoogle Scholar
  12. 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 117:4253–4264CrossRefPubMedGoogle Scholar
  13. Ehrenhofer-Murray AE (2004) Chromatin dynamics at DNA replication, transcription and repair. Eur J Biochem 271:2335–2349CrossRefPubMedGoogle Scholar
  14. Ehrenhofer-Murray AE, Rivier DH, Rine J (1997) The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function. Genetics 145:923–934PubMedGoogle Scholar
  15. 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 281:17968–17976CrossRefPubMedGoogle Scholar
  16. 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 4:575–580CrossRefPubMedGoogle Scholar
  17. Gallant P (2007) Control of transcription by Pontin and Reptin. Trends Cell Biol 17:187–192CrossRefPubMedGoogle Scholar
  18. 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 276:46841–46848CrossRefPubMedGoogle Scholar
  19. 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 26:2347–2359CrossRefPubMedGoogle Scholar
  20. Gavaravarapu S, Kamine J (2000) Tip60 inhibits activation of CREB protein by protein kinase A. Biochem Biophys Res Commun 269:758–766CrossRefPubMedGoogle Scholar
  21. 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 448:1063–1067CrossRefPubMedGoogle Scholar
  22. 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 114:54–66CrossRefPubMedGoogle Scholar
  23. 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 12:762–766CrossRefPubMedGoogle Scholar
  24. Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293–296CrossRefPubMedGoogle Scholar
  25. 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 132:1819–1830CrossRefPubMedGoogle Scholar
  26. 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 102:463–473CrossRefPubMedGoogle Scholar
  27. 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 216:357–366CrossRefPubMedGoogle Scholar
  28. 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 236:404–415CrossRefPubMedGoogle Scholar
  29. 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 27:6506–6519CrossRefPubMedGoogle Scholar
  30. 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 32:370–377CrossRefPubMedGoogle Scholar
  31. 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 133:813–828CrossRefPubMedGoogle Scholar
  32. Kramer JM, Staveley BE (2003) GAL4 causes developmental defects and apoptosis when expressed in the developing eye of Drosophila melanogaster. Genet Mol Res 2:43–47PubMedGoogle Scholar
  33. 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 306:2084–2087CrossRefPubMedGoogle Scholar
  34. 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 279:44825–44833CrossRefPubMedGoogle Scholar
  35. 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 15:3169–3182CrossRefPubMedGoogle Scholar
  36. Mendjan S, Akhtar A (2007) The right dose for every sex. Chromosoma 116:95–106CrossRefPubMedGoogle Scholar
  37. 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 20:101–112CrossRefPubMedGoogle Scholar
  38. 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 154:657–668PubMedGoogle Scholar
  39. 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 314:654–657CrossRefPubMedGoogle Scholar
  40. 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 117:151–162CrossRefPubMedGoogle Scholar
  41. 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 5:49–51CrossRefPubMedGoogle Scholar
  42. 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 24:10826–10834CrossRefPubMedGoogle Scholar
  43. Qi D, Jin H, Lilja T, Mannervik M (2006) Drosophila Reptin and other TIP60 complex components promote generation of silent chromatin. Genetics 174:241–251CrossRefPubMedGoogle Scholar
  44. R Development Core Team (2008) R: A language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
  45. 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 14:42–49CrossRefPubMedGoogle Scholar
  46. 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 118:461–470PubMedGoogle Scholar
  47. Sanjuan R, Marin I (2001) Tracing the origin of the compensasome: evolutionary history of DEAH helicase and MYST acetyltransferase gene families. Mol Biol Evol 18:330–343PubMedGoogle Scholar
  48. Sapountzi V, Logan IR, Robson CN (2006) Cellular functions of TIP60. Int J Biochem Cell Biol 38:1496–1509CrossRefPubMedGoogle Scholar
  49. 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 20:2507–2512CrossRefPubMedGoogle Scholar
  50. Squatrito M, Gorrini C, Amati B (2006) Tip60 in DNA damage response and growth control: many tricks in one HAT. Trends Cell Biol 16:433–442CrossRefPubMedGoogle Scholar
  51. Suka N, Luo K, Grunstein M (2002) Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin. Nat Genet 32:378–383CrossRefPubMedGoogle Scholar
  52. 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 19:65–76CrossRefPubMedGoogle Scholar
  53. 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 24:841–851CrossRefPubMedGoogle Scholar
  54. 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 24:827–839CrossRefPubMedGoogle Scholar
  55. 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 24:4546–4556CrossRefPubMedGoogle Scholar
  56. 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 98:81–85CrossRefPubMedGoogle Scholar
  57. Utley RT, Cote J (2003) The MYST family of histone acetyltransferases. Curr Top Microbiol Immunol 274:203–236PubMedGoogle Scholar
  58. 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 17:1402–1414CrossRefPubMedGoogle Scholar
  59. Xiao H, Chung J, Kao HY, Yang YC (2003) Tip60 is a co-repressor for STAT3. J Biol Chem 278:11197–11204CrossRefPubMedGoogle Scholar
  60. 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 175:1229–1240CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Corinna Schirling
    • 1
  • Christiane Heseding
    • 1
  • Franziska Heise
    • 1
  • Dörthe Kesper
    • 2
  • Ansgar Klebes
    • 4
  • Ludger Klein-Hitpass
    • 5
  • Andrea Vortkamp
    • 2
  • Daniel Hoffmann
    • 3
  • Harald Saumweber
    • 6
  • Ann E. Ehrenhofer-Murray
    • 1
  1. 1.Abteilung für Genetik, Zentrum für Medizinische BiotechnologieUniversität Duisburg-EssenEssenGermany
  2. 2.Abteilung für Entwicklungsbiologie, Zentrum für Medizinische BiotechnologieUniversität Duisburg-EssenEssenGermany
  3. 3.Abteilung für Bioinformatik, Zentrum für Medizinische BiotechnologieUniversität Duisburg-EssenEssenGermany
  4. 4.Institut für Biologie-GenetikFreie Universität BerlinBerlinGermany
  5. 5.Institut für ZellbiologieUniversitätsklinikumEssenGermany
  6. 6.Abteilung Zytogenetik, Institut für BiologieHumboldt Universität BerlinBerlinGermany

Personalised recommendations