Abstract
The Saccharomyces cerevisiae Sin3 transcriptional repressor is part of a large multiprotein complex that includes the Rpd3 histone deacetylase. A LexA-Sin3 fusion protein represses transcription of promoters with LexA binding sites. To identify genes involved in repression by Sin3, we conducted a screen for mutations that reduce repression by LexA-Sin3. One of the mutations identified that reduces LexA-Sin3 repression is in the RPD3 gene, consistent with the known roles of Rpd3 in transcriptional repression. Mutations in CBK1 and HYM1 reduce repression by LexA-Sin3 and also cause defects in cell separation and altered colony morphology. cbk1 and hym1 mutations affect some but not all genes regulated by SIN3 and RPD3, but the effect on transcription is much weaker. Genetic analysis suggests that CBK1 and HYM1 function in the same pathway, but this genetic pathway is separable from that of SIN3 and RPD3. The remaining gene from this screen described in this report is SDS3, previously identified in a screen for mutations that increase silencing at HML, HMR, and telomere-linked genes, a phenotype also seen in sin3 and rpd3 mutants. Genetic analysis demonstrates that SDS3 functions in the same genetic pathway as SIN3 and RPD3, and coimmunoprecipitation experiments show that Sds3 is physically present in the Sin3 complex.
Full Text
The Full Text of this article is available as a PDF (239.0 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Alland L., Muhle R., Hou H., Jr, Potes J., Chin L., Schreiber-Agus N., DePinho R. A. Role for N-CoR and histone deacetylase in Sin3-mediated transcriptional repression. Nature. 1997 May 1;387(6628):49–55. doi: 10.1038/387049a0. [DOI] [PubMed] [Google Scholar]
- Aparicio O. M., Billington B. L., Gottschling D. E. Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell. 1991 Sep 20;66(6):1279–1287. doi: 10.1016/0092-8674(91)90049-5. [DOI] [PubMed] [Google Scholar]
- Brachmann C. B., Davies A., Cost G. J., Caputo E., Li J., Hieter P., Boeke J. D. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast. 1998 Jan 30;14(2):115–132. doi: 10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2. [DOI] [PubMed] [Google Scholar]
- Breeden L., Nasmyth K. Cell cycle control of the yeast HO gene: cis- and trans-acting regulators. Cell. 1987 Feb 13;48(3):389–397. doi: 10.1016/0092-8674(87)90190-5. [DOI] [PubMed] [Google Scholar]
- Cairns B. R., Levinson R. S., Yamamoto K. R., Kornberg R. D. Essential role of Swp73p in the function of yeast Swi/Snf complex. Genes Dev. 1996 Sep 1;10(17):2131–2144. doi: 10.1101/gad.10.17.2131. [DOI] [PubMed] [Google Scholar]
- De Rubertis F., Kadosh D., Henchoz S., Pauli D., Reuter G., Struhl K., Spierer P. The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature. 1996 Dec 12;384(6609):589–591. doi: 10.1038/384589a0. [DOI] [PubMed] [Google Scholar]
- Gottschling D. E., Aparicio O. M., Billington B. L., Zakian V. A. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell. 1990 Nov 16;63(4):751–762. doi: 10.1016/0092-8674(90)90141-z. [DOI] [PubMed] [Google Scholar]
- Hampsey M. A SAGA of histone acetylation and gene expression. Trends Genet. 1997 Nov;13(11):427–429. doi: 10.1016/s0168-9525(97)01292-4. [DOI] [PubMed] [Google Scholar]
- Han M., Kim U. J., Kayne P., Grunstein M. Depletion of histone H4 and nucleosomes activates the PHO5 gene in Saccharomyces cerevisiae. EMBO J. 1988 Jul;7(7):2221–2228. doi: 10.1002/j.1460-2075.1988.tb03061.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hassig C. A., Fleischer T. C., Billin A. N., Schreiber S. L., Ayer D. E. Histone deacetylase activity is required for full transcriptional repression by mSin3A. Cell. 1997 May 2;89(3):341–347. doi: 10.1016/s0092-8674(00)80214-7. [DOI] [PubMed] [Google Scholar]
- Heinzel T., Lavinsky R. M., Mullen T. M., Söderstrom M., Laherty C. D., Torchia J., Yang W. M., Brard G., Ngo S. D., Davie J. R. A complex containing N-CoR, mSin3 and histone deacetylase mediates transcriptional repression. Nature. 1997 May 1;387(6628):43–48. doi: 10.1038/387043a0. [DOI] [PubMed] [Google Scholar]
- Hepworth S. R., Friesen H., Segall J. NDT80 and the meiotic recombination checkpoint regulate expression of middle sporulation-specific genes in Saccharomyces cerevisiae. Mol Cell Biol. 1998 Oct;18(10):5750–5761. doi: 10.1128/mcb.18.10.5750. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hill J. E., Myers A. M., Koerner T. J., Tzagoloff A. Yeast/E. coli shuttle vectors with multiple unique restriction sites. Yeast. 1986 Sep;2(3):163–167. doi: 10.1002/yea.320020304. [DOI] [PubMed] [Google Scholar]
- Hudak K. A., Lopes J. M., Henry S. A. A pleiotropic phospholipid biosynthetic regulatory mutation in Saccharomyces cerevisiae is allelic to sin3 (sdi1, ume4, rpd1). Genetics. 1994 Feb;136(2):475–483. doi: 10.1093/genetics/136.2.475. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hunter T., Plowman G. D. The protein kinases of budding yeast: six score and more. Trends Biochem Sci. 1997 Jan;22(1):18–22. doi: 10.1016/s0968-0004(96)10068-2. [DOI] [PubMed] [Google Scholar]
- Kadonaga J. T. Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines. Cell. 1998 Feb 6;92(3):307–313. doi: 10.1016/s0092-8674(00)80924-1. [DOI] [PubMed] [Google Scholar]
- Kadosh D., Struhl K. Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo. Genes Dev. 1998 Mar 15;12(6):797–805. doi: 10.1101/gad.12.6.797. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kadosh D., Struhl K. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell. 1997 May 2;89(3):365–371. doi: 10.1016/s0092-8674(00)80217-2. [DOI] [PubMed] [Google Scholar]
- Kadosh D., Struhl K. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol Cell Biol. 1998 Sep;18(9):5121–5127. doi: 10.1128/mcb.18.9.5121. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Karos M., Fischer R. Molecular characterization of HymA, an evolutionarily highly conserved and highly expressed protein of Aspergillus nidulans. Mol Gen Genet. 1999 Jan;260(6):510–521. doi: 10.1007/s004380050924. [DOI] [PubMed] [Google Scholar]
- Kasten M. M., Ayer D. E., Stillman D. J. SIN3-dependent transcriptional repression by interaction with the Mad1 DNA-binding protein. Mol Cell Biol. 1996 Aug;16(8):4215–4221. doi: 10.1128/mcb.16.8.4215. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Laherty C. D., Yang W. M., Sun J. M., Davie J. R., Seto E., Eisenman R. N. Histone deacetylases associated with the mSin3 corepressor mediate mad transcriptional repression. Cell. 1997 May 2;89(3):349–356. doi: 10.1016/s0092-8674(00)80215-9. [DOI] [PubMed] [Google Scholar]
- Longtine M. S., McKenzie A., 3rd, Demarini D. J., Shah N. G., Wach A., Brachat A., Philippsen P., Pringle J. R. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast. 1998 Jul;14(10):953–961. doi: 10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U. [DOI] [PubMed] [Google Scholar]
- Nagy L., Kao H. Y., Chakravarti D., Lin R. J., Hassig C. A., Ayer D. E., Schreiber S. L., Evans R. M. Nuclear receptor repression mediated by a complex containing SMRT, mSin3A, and histone deacetylase. Cell. 1997 May 2;89(3):373–380. doi: 10.1016/s0092-8674(00)80218-4. [DOI] [PubMed] [Google Scholar]
- Nasmyth K., Stillman D., Kipling D. Both positive and negative regulators of HO transcription are required for mother-cell-specific mating-type switching in yeast. Cell. 1987 Feb 27;48(4):579–587. doi: 10.1016/0092-8674(87)90236-4. [DOI] [PubMed] [Google Scholar]
- Pazin M. J., Kadonaga J. T. What's up and down with histone deacetylation and transcription? Cell. 1997 May 2;89(3):325–328. doi: 10.1016/s0092-8674(00)80211-1. [DOI] [PubMed] [Google Scholar]
- Renauld H., Aparicio O. M., Zierath P. D., Billington B. L., Chhablani S. K., Gottschling D. E. Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage. Genes Dev. 1993 Jul;7(7A):1133–1145. doi: 10.1101/gad.7.7a.1133. [DOI] [PubMed] [Google Scholar]
- Rundlett S. E., Carmen A. A., Kobayashi R., Bavykin S., Turner B. M., Grunstein M. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14503–14508. doi: 10.1073/pnas.93.25.14503. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rundlett S. E., Carmen A. A., Suka N., Turner B. M., Grunstein M. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature. 1998 Apr 23;392(6678):831–835. doi: 10.1038/33952. [DOI] [PubMed] [Google Scholar]
- Stillman D. J., Dorland S., Yu Y. Epistasis analysis of suppressor mutations that allow HO expression in the absence of the yeast SW15 transcriptional activator. Genetics. 1994 Mar;136(3):781–788. doi: 10.1093/genetics/136.3.781. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Struhl K. Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 1998 Mar 1;12(5):599–606. doi: 10.1101/gad.12.5.599. [DOI] [PubMed] [Google Scholar]
- Sun Z. W., Hampsey M. A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics. 1999 Jul;152(3):921–932. doi: 10.1093/genetics/152.3.921. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sussel L., Vannier D., Shore D. Suppressors of defective silencing in yeast: effects on transcriptional repression at the HMR locus, cell growth and telomere structure. Genetics. 1995 Nov;141(3):873–888. doi: 10.1093/genetics/141.3.873. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Taunton J., Hassig C. A., Schreiber S. L. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science. 1996 Apr 19;272(5260):408–411. doi: 10.1126/science.272.5260.408. [DOI] [PubMed] [Google Scholar]
- Thomas B. J., Rothstein R. Elevated recombination rates in transcriptionally active DNA. Cell. 1989 Feb 24;56(4):619–630. doi: 10.1016/0092-8674(89)90584-9. [DOI] [PubMed] [Google Scholar]
- To-E A., Ueda Y., Kakimoto S. I., Oshima Y. Isolation and characterization of acid phosphatase mutants in Saccharomyces cerevisiae. J Bacteriol. 1973 Feb;113(2):727–738. doi: 10.1128/jb.113.2.727-738.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vannier D., Balderes D., Shore D. Evidence that the transcriptional regulators SIN3 and RPD3, and a novel gene (SDS3) with similar functions, are involved in transcriptional silencing in S. cerevisiae. Genetics. 1996 Dec;144(4):1343–1353. doi: 10.1093/genetics/144.4.1343. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vidal M., Buckley A. M., Hilger F., Gaber R. F. Direct selection for mutants with increased K+ transport in Saccharomyces cerevisiae. Genetics. 1990 Jun;125(2):313–320. doi: 10.1093/genetics/125.2.313. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vidal M., Gaber R. F. RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae. Mol Cell Biol. 1991 Dec;11(12):6317–6327. doi: 10.1128/mcb.11.12.6317. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vidal M., Gaber R. F. Selectable marker replacement in Saccharomyces cerevisiae. Yeast. 1994 Feb;10(2):141–149. doi: 10.1002/yea.320100202. [DOI] [PubMed] [Google Scholar]
- Vidal M., Strich R., Esposito R. E., Gaber R. F. RPD1 (SIN3/UME4) is required for maximal activation and repression of diverse yeast genes. Mol Cell Biol. 1991 Dec;11(12):6306–6316. doi: 10.1128/mcb.11.12.6306. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang H., Reynolds-Hager L., Stillman D. J. Genetic interactions between SIN3 mutations and the Saccharomyces cerevisiae transcriptional activators encoded by MCM1, STE12, and SWI1. Mol Gen Genet. 1994 Dec 15;245(6):675–685. doi: 10.1007/BF00297274. [DOI] [PubMed] [Google Scholar]
- Wolffe A. P., Pruss D. Targeting chromatin disruption: Transcription regulators that acetylate histones. Cell. 1996 Mar 22;84(6):817–819. doi: 10.1016/s0092-8674(00)81059-4. [DOI] [PubMed] [Google Scholar]
- Wolffe A. P. Transcriptional control. Sinful repression. Nature. 1997 May 1;387(6628):16–17. doi: 10.1038/387016a0. [DOI] [PubMed] [Google Scholar]
- Zhang Y., Iratni R., Erdjument-Bromage H., Tempst P., Reinberg D. Histone deacetylases and SAP18, a novel polypeptide, are components of a human Sin3 complex. Cell. 1997 May 2;89(3):357–364. doi: 10.1016/s0092-8674(00)80216-0. [DOI] [PubMed] [Google Scholar]
- Zhang Y., Sun Z. W., Iratni R., Erdjument-Bromage H., Tempst P., Hampsey M., Reinberg D. SAP30, a novel protein conserved between human and yeast, is a component of a histone deacetylase complex. Mol Cell. 1998 Jun;1(7):1021–1031. doi: 10.1016/s1097-2765(00)80102-1. [DOI] [PubMed] [Google Scholar]