Abstract
A dominant insertional P-element mutation enhances position-effect variegation in Drosophila melanogaster. The mutation is homozygous, viable, and fertile and maps at 64E on the third chromosome. The corresponding gene was cloned by transposon tagging. Insertion of the transposon upstream of the open reading frame correlates with a strong reduction of transcript level. A transgene was constructed with the cDNA and found to have the effect opposite from that of the mutation, namely, to suppress variegation. Sequencing of the cDNA reveals a large open reading frame encoding a putative ubiquitin-specific protease (Ubp). Ubiquitin marks various proteins, frequently for proteasome-dependent degradation. Ubps can cleave the ubiquitin part from these proteins. We discuss the link established here between a deubiquitinating enzyme and epigenetic silencing processes.
Full Text
The Full Text of this article is available as a PDF (2.6 MB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Baker R. T., Tobias J. W., Varshavsky A. Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family. J Biol Chem. 1992 Nov 15;267(32):23364–23375. [PubMed] [Google Scholar]
- Baksa K., Morawietz H., Dombrádi V., Axton M., Taubert H., Szabó G., Török I., Udvardy A., Gyurkovics H., Ször B. Mutations in the protein phosphatase 1 gene at 87B can differentially affect suppression of position-effect variegation and mitosis in Drosophila melanogaster. Genetics. 1993 Sep;135(1):117–125. doi: 10.1093/genetics/135.1.117. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bishop C. P. Evidence for intrinsic differences in the formation of chromatin domains in Drosophila melanogaster. Genetics. 1992 Dec;132(4):1063–1069. doi: 10.1093/genetics/132.4.1063. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brown N. H., Kafatos F. C. Functional cDNA libraries from Drosophila embryos. J Mol Biol. 1988 Sep 20;203(2):425–437. doi: 10.1016/0022-2836(88)90010-1. [DOI] [PubMed] [Google Scholar]
- Busch H. Ubiquitination of proteins. Methods Enzymol. 1984;106:238–262. doi: 10.1016/0076-6879(84)06025-0. [DOI] [PubMed] [Google Scholar]
- Ciechanover A. The ubiquitin-proteasome proteolytic pathway. Cell. 1994 Oct 7;79(1):13–21. doi: 10.1016/0092-8674(94)90396-4. [DOI] [PubMed] [Google Scholar]
- Cléard F., Matsarskaia M., Spierer P. The modifier of position-effect variegation Suvar(3)7 of Drosophila: there are two alternative transcripts and seven scattered zinc fingers, each preceded by a tryptophan box. Nucleic Acids Res. 1995 Mar 11;23(5):796–802. doi: 10.1093/nar/23.5.796. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Davie J. R., Murphy L. C. Inhibition of transcription selectively reduces the level of ubiquitinated histone H2B in chromatin. Biochem Biophys Res Commun. 1994 Aug 30;203(1):344–350. doi: 10.1006/bbrc.1994.2188. [DOI] [PubMed] [Google Scholar]
- Davies N., Lindsey G. G. Histone H2B (and H2A) ubiquitination allows normal histone octamer and core particle reconstitution. Biochim Biophys Acta. 1994 Jun 21;1218(2):187–193. doi: 10.1016/0167-4781(94)90009-4. [DOI] [PubMed] [Google Scholar]
- Dolfini S. Karyotype polymorphism in a cell population of Drosophila melanogaster cultured in vitro. Chromosoma. 1971;33(2):196–208. doi: 10.1007/BF00285633. [DOI] [PubMed] [Google Scholar]
- Dorn R., Krauss V., Reuter G., Saumweber H. The enhancer of position-effect variegation of Drosophila, E(var)3-93D, codes for a chromatin protein containing a conserved domain common to several transcriptional regulators. Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):11376–11380. doi: 10.1073/pnas.90.23.11376. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dorn R., Szidonya J., Korge G., Sehnert M., Taubert H., Archoukieh E., Tschiersch B., Morawietz H., Wustmann G., Hoffmann G. P transposon-induced dominant enhancer mutations of position-effect variegation in Drosophila melanogaster. Genetics. 1993 Feb;133(2):279–290. doi: 10.1093/genetics/133.2.279. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eissenberg J. C., James T. C., Foster-Hartnett D. M., Hartnett T., Ngan V., Elgin S. C. Mutation in a heterochromatin-specific chromosomal protein is associated with suppression of position-effect variegation in Drosophila melanogaster. Proc Natl Acad Sci U S A. 1990 Dec;87(24):9923–9927. doi: 10.1073/pnas.87.24.9923. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eissenberg J. C. Position effect variegation in Drosophila: towards a genetics of chromatin assembly. Bioessays. 1989 Jul;11(1):14–17. doi: 10.1002/bies.950110105. [DOI] [PubMed] [Google Scholar]
- Falquet L., Paquet N., Frutiger S., Hughes G. J., Hoang-Van K., Jaton J. C. cDNA cloning of a human 100 kDa de-ubiquitinating enzyme: the 100 kDa human de-ubiquitinase belongs to the ubiquitin C-terminal hydrolase family 2 (UCH2). FEBS Lett. 1995 Dec 4;376(3):233–237. doi: 10.1016/0014-5793(95)01287-7. [DOI] [PubMed] [Google Scholar]
- Farkas G., Gausz J., Galloni M., Reuter G., Gyurkovics H., Karch F. The Trithorax-like gene encodes the Drosophila GAGA factor. Nature. 1994 Oct 27;371(6500):806–808. doi: 10.1038/371806a0. [DOI] [PubMed] [Google Scholar]
- Fauvarque M. O., Dura J. M. polyhomeotic regulatory sequences induce developmental regulator-dependent variegation and targeted P-element insertions in Drosophila. Genes Dev. 1993 Aug;7(8):1508–1520. doi: 10.1101/gad.7.8.1508. [DOI] [PubMed] [Google Scholar]
- Fischer-Vize J. A., Rubin G. M., Lehmann R. The fat facets gene is required for Drosophila eye and embryo development. Development. 1992 Dec;116(4):985–1000. doi: 10.1242/dev.116.4.985. [DOI] [PubMed] [Google Scholar]
- Glotzer M. Cell cycle. The only way out of mitosis. Curr Biol. 1995 Sep 1;5(9):970–972. doi: 10.1016/s0960-9822(95)00190-4. [DOI] [PubMed] [Google Scholar]
- Goldstein G., Scheid M., Hammerling U., Schlesinger D. H., Niall H. D., Boyse E. A. Isolation of a polypeptide that has lymphocyte-differentiating properties and is probably represented universally in living cells. Proc Natl Acad Sci U S A. 1975 Jan;72(1):11–15. doi: 10.1073/pnas.72.1.11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Grossniklaus U., Bellen H. J., Wilson C., Gehring W. J. P-element-mediated enhancer detection applied to the study of oogenesis in Drosophila. Development. 1989 Oct;107(2):189–200. doi: 10.1242/dev.107.2.189. [DOI] [PubMed] [Google Scholar]
- Hayashi S., Ruddell A., Sinclair D., Grigliatti T. Chromosomal structure is altered by mutations that suppress or enhance position effect variegation. Chromosoma. 1990 Oct;99(6):391–400. doi: 10.1007/BF01726690. [DOI] [PubMed] [Google Scholar]
- Henderson D. S., Banga S. S., Grigliatti T. A., Boyd J. B. Mutagen sensitivity and suppression of position-effect variegation result from mutations in mus209, the Drosophila gene encoding PCNA. EMBO J. 1994 Mar 15;13(6):1450–1459. doi: 10.1002/j.1460-2075.1994.tb06399.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hendrich B. D., Willard H. F. Epigenetic regulation of gene expression: the effect of altered chromatin structure from yeast to mammals. Hum Mol Genet. 1995;4(Spec No):1765–1777. doi: 10.1093/hmg/4.suppl_1.1765. [DOI] [PubMed] [Google Scholar]
- Henikoff S. Position-effect variegation after 60 years. Trends Genet. 1990 Dec;6(12):422–426. doi: 10.1016/0168-9525(90)90304-o. [DOI] [PubMed] [Google Scholar]
- Hochstrasser M. Ubiquitin, proteasomes, and the regulation of intracellular protein degradation. Curr Opin Cell Biol. 1995 Apr;7(2):215–223. doi: 10.1016/0955-0674(95)80031-x. [DOI] [PubMed] [Google Scholar]
- Huang Y., Baker R. T., Fischer-Vize J. A. Control of cell fate by a deubiquitinating enzyme encoded by the fat facets gene. Science. 1995 Dec 15;270(5243):1828–1831. doi: 10.1126/science.270.5243.1828. [DOI] [PubMed] [Google Scholar]
- Karpen G. H., Spradling A. C. Reduced DNA polytenization of a minichromosome region undergoing position-effect variegation in Drosophila. Cell. 1990 Oct 5;63(1):97–107. doi: 10.1016/0092-8674(90)90291-l. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kornberg R. D., Lorch Y. Interplay between chromatin structure and transcription. Curr Opin Cell Biol. 1995 Jun;7(3):371–375. doi: 10.1016/0955-0674(95)80092-1. [DOI] [PubMed] [Google Scholar]
- Laman H., Balderes D., Shore D. Disturbance of normal cell cycle progression enhances the establishment of transcriptional silencing in Saccharomyces cerevisiae. Mol Cell Biol. 1995 Jul;15(7):3608–3617. doi: 10.1128/mcb.15.7.3608. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Levinger L., Varshavsky A. Selective arrangement of ubiquitinated and D1 protein-containing nucleosomes within the Drosophila genome. Cell. 1982 Feb;28(2):375–385. doi: 10.1016/0092-8674(82)90355-5. [DOI] [PubMed] [Google Scholar]
- Locke J., Kotarski M. A., Tartof K. D. Dosage-dependent modifiers of position effect variegation in Drosophila and a mass action model that explains their effect. Genetics. 1988 Sep;120(1):181–198. doi: 10.1093/genetics/120.1.181. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maniatis T., Hardison R. C., Lacy E., Lauer J., O'Connell C., Quon D., Sim G. K., Efstratiadis A. The isolation of structural genes from libraries of eucaryotic DNA. Cell. 1978 Oct;15(2):687–701. doi: 10.1016/0092-8674(78)90036-3. [DOI] [PubMed] [Google Scholar]
- Moehrle A., Paro R. Spreading the silence: epigenetic transcriptional regulation during Drosophila development. Dev Genet. 1994;15(6):478–484. doi: 10.1002/dvg.1020150606. [DOI] [PubMed] [Google Scholar]
- Monaco J. J., Nandi D. The genetics of proteasomes and antigen processing. Annu Rev Genet. 1995;29:729–754. doi: 10.1146/annurev.ge.29.120195.003501. [DOI] [PubMed] [Google Scholar]
- Nakamura T., Hillova J., Mariage-Samson R., Onno M., Huebner K., Cannizzaro L. A., Boghosian-Sell L., Croce C. M., Hill M. A novel transcriptional unit of the tre oncogene widely expressed in human cancer cells. Oncogene. 1992 Apr;7(4):733–741. [PubMed] [Google Scholar]
- Palombella V. J., Rando O. J., Goldberg A. L., Maniatis T. The ubiquitin-proteasome pathway is required for processing the NF-kappa B1 precursor protein and the activation of NF-kappa B. Cell. 1994 Sep 9;78(5):773–785. doi: 10.1016/s0092-8674(94)90482-0. [DOI] [PubMed] [Google Scholar]
- Papa F. R., Hochstrasser M. The yeast DOA4 gene encodes a deubiquitinating enzyme related to a product of the human tre-2 oncogene. Nature. 1993 Nov 25;366(6453):313–319. doi: 10.1038/366313a0. [DOI] [PubMed] [Google Scholar]
- Paro R., Hogness D. S. The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):263–267. doi: 10.1073/pnas.88.1.263. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pickart C. M., Rose I. A. Mechanism of ubiquitin carboxyl-terminal hydrolase. Borohydride and hydroxylamine inactivate in the presence of ubiquitin. J Biol Chem. 1986 Aug 5;261(22):10210–10217. [PubMed] [Google Scholar]
- Ramos R. G., Igloi G. L., Lichte B., Baumann U., Maier D., Schneider T., Brandstätter J. H., Fröhlich A., Fischbach K. F. The irregular chiasm C-roughest locus of Drosophila, which affects axonal projections and programmed cell death, encodes a novel immunoglobulin-like protein. Genes Dev. 1993 Dec;7(12B):2533–2547. doi: 10.1101/gad.7.12b.2533. [DOI] [PubMed] [Google Scholar]
- Reuter G., Giarre M., Farah J., Gausz J., Spierer A., Spierer P. Dependence of position-effect variegation in Drosophila on dose of a gene encoding an unusual zinc-finger protein. Nature. 1990 Mar 15;344(6263):219–223. doi: 10.1038/344219a0. [DOI] [PubMed] [Google Scholar]
- Reuter G., Spierer P. Position effect variegation and chromatin proteins. Bioessays. 1992 Sep;14(9):605–612. doi: 10.1002/bies.950140907. [DOI] [PubMed] [Google Scholar]
- Reuter G., Werner W., Hoffmann H. J. Mutants affecting position-effect heterochromatinization in Drosophila melanogaster. Chromosoma. 1982;85(4):539–551. doi: 10.1007/BF00327349. [DOI] [PubMed] [Google Scholar]
- Reuter G., Wolff I. Isolation of dominant suppressor mutations for position-effect variegation in Drosophila melanogaster. Mol Gen Genet. 1981;182(3):516–519. doi: 10.1007/BF00293947. [DOI] [PubMed] [Google Scholar]
- Saville K. J., Belote J. M. Identification of an essential gene, l(3)73Ai, with a dominant temperature-sensitive lethal allele, encoding a Drosophila proteasome subunit. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):8842–8846. doi: 10.1073/pnas.90.19.8842. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schneuwly S., Kuroiwa A., Baumgartner P., Gehring W. J. Structural organization and sequence of the homeotic gene Antennapedia of Drosophila melanogaster. EMBO J. 1986 Apr;5(4):733–739. doi: 10.1002/j.1460-2075.1986.tb04275.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Seifert H. S., Chen E. Y., So M., Heffron F. Shuttle mutagenesis: a method of transposon mutagenesis for Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1986 Feb;83(3):735–739. doi: 10.1073/pnas.83.3.735. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Seufert W., Futcher B., Jentsch S. Role of a ubiquitin-conjugating enzyme in degradation of S- and M-phase cyclins. Nature. 1995 Jan 5;373(6509):78–81. doi: 10.1038/373078a0. [DOI] [PubMed] [Google Scholar]
- Seum C., Spierer A., Pauli D., Szidonya J., Reuter G., Spierer P. Position-effect variegation in Drosophila depends on dose of the gene encoding the E2F transcriptional activator and cell cycle regulator. Development. 1996 Jun;122(6):1949–1956. doi: 10.1242/dev.122.6.1949. [DOI] [PubMed] [Google Scholar]
- Siegelman M., Bond M. W., Gallatin W. M., St John T., Smith H. T., Fried V. A., Weissman I. L. Cell surface molecule associated with lymphocyte homing is a ubiquitinated branched-chain glycoprotein. Science. 1986 Feb 21;231(4740):823–829. doi: 10.1126/science.3003913. [DOI] [PubMed] [Google Scholar]
- Soeller W. C., Oh C. E., Kornberg T. B. Isolation of cDNAs encoding the Drosophila GAGA transcription factor. Mol Cell Biol. 1993 Dec;13(12):7961–7970. doi: 10.1128/mcb.13.12.7961. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
- Spierer P., Spierer A., Bender W., Hogness D. S. Molecular mapping of genetic and chromomeric units in Drosophila melanogaster. J Mol Biol. 1983 Jul 25;168(1):35–50. doi: 10.1016/s0022-2836(83)80321-0. [DOI] [PubMed] [Google Scholar]
- Tamkun J. W., Deuring R., Scott M. P., Kissinger M., Pattatucci A. M., Kaufman T. C., Kennison J. A. brahma: a regulator of Drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2/SWI2. Cell. 1992 Feb 7;68(3):561–572. doi: 10.1016/0092-8674(92)90191-e. [DOI] [PubMed] [Google Scholar]
- Tartof K. D., Bishop C., Jones M., Hobbs C. A., Locke J. Towards an understanding of position effect variegation. Dev Genet. 1989;10(3):162–176. doi: 10.1002/dvg.1020100306. [DOI] [PubMed] [Google Scholar]
- Tartof K. D., Hobbs C., Jones M. A structural basis for variegating position effects. Cell. 1984 Jul;37(3):869–878. doi: 10.1016/0092-8674(84)90422-7. [DOI] [PubMed] [Google Scholar]
- Tautz D., Pfeifle C. 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. 1989 Aug;98(2):81–85. doi: 10.1007/BF00291041. [DOI] [PubMed] [Google Scholar]
- Tschiersch B., Hofmann A., Krauss V., Dorn R., Korge G., Reuter G. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J. 1994 Aug 15;13(16):3822–3831. doi: 10.1002/j.1460-2075.1994.tb06693.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tsukiyama T., Daniel C., Tamkun J., Wu C. ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor. Cell. 1995 Dec 15;83(6):1021–1026. doi: 10.1016/0092-8674(95)90217-1. [DOI] [PubMed] [Google Scholar]
- Vijay-Kumar S., Bugg C. E., Wilkinson K. D., Vierstra R. D., Hatfield P. M., Cook W. J. Comparison of the three-dimensional structures of human, yeast, and oat ubiquitin. J Biol Chem. 1987 May 5;262(13):6396–6399. [PubMed] [Google Scholar]
- Wilkinson K. D., Tashayev V. L., O'Connor L. B., Larsen C. N., Kasperek E., Pickart C. M. Metabolism of the polyubiquitin degradation signal: structure, mechanism, and role of isopeptidase T. Biochemistry. 1995 Nov 7;34(44):14535–14546. doi: 10.1021/bi00044a032. [DOI] [PubMed] [Google Scholar]
- Xiao W., Fontanie T., Tang M. UBP5 encodes a putative yeast ubiquitin-specific protease that is related to the human Tre-2 oncogene product. Yeast. 1994 Nov;10(11):1497–1502. doi: 10.1002/yea.320101114. [DOI] [PubMed] [Google Scholar]
- Yarden Y., Escobedo J. A., Kuang W. J., Yang-Feng T. L., Daniel T. O., Tremble P. M., Chen E. Y., Ando M. E., Harkins R. N., Francke U. Structure of the receptor for platelet-derived growth factor helps define a family of closely related growth factor receptors. Nature. 1986 Sep 18;323(6085):226–232. doi: 10.1038/323226a0. [DOI] [PubMed] [Google Scholar]
- Zhang N., Wilkinson K., Bownes M. Cloning and analysis of expression of a ubiquitin carboxyl terminal hydrolase expressed during oogenesis in Drosophila melanogaster. Dev Biol. 1993 May;157(1):214–223. doi: 10.1006/dbio.1993.1125. [DOI] [PubMed] [Google Scholar]