Home LiteratureArticle Details
PMID: 11711434 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program.

Genes & development ·Vol. 15 ·No. 22 ·2001-11-15 ·Pages 2991-3004

Pijnappel WW, Schaft D, Roguev A, Shevchenko A, Tekotte H, Wilm M, Rigaut G, Séraphin B, Aasland R, Stewart AF

Abstract

Set3 is one of two proteins in the yeast Saccharomyces cerevisiae that, like Drosophila Trithorax, contains both SET and PHD domains. We found that Set3 forms a single complex, Set3C, with Snt1, YIL112w, Sif2, Cpr1, and two putative histone deacetylases, Hos2 and NAD-dependent Hst1. Set3C includes NAD-dependent and independent deacetylase activities when assayed in vitro. Homology searches suggest that Set3C is the yeast analog of the mammalian HDAC3/SMRT complex. Set3C represses genes in early/middle of the yeast sporulation program, including the key meiotic regulators ime2 and ndt80. Whereas Hos2 is only found in Set3C, Hst1 is also present in a complex with Sum1, supporting previous characterizations of Hst1 and Sum1 as repressors of middle sporulation genes during vegetative growth. However, Hst1 is not required for meiotic repression by Set3C, thus implying that Set3C (-Hst1) and not Hst1-Sum1, is the meiotic-specific repressor of early/middle sporulation genes.

MeSH Terms
Amino Acid Sequence Fungal Proteins/chemistry Haploidy Histone Deacetylases/metabolism Mass Spectrometry Meiosis Molecular Sequence Data Phenotype Precipitin Tests Protein Binding Protein Structure, Tertiary Saccharomyces cerevisiae/chemistry,genetics Saccharomyces cerevisiae Proteins/metabolism Schizosaccharomyces pombe Proteins Sirtuin 2 Sirtuins Time Factors
Chemicals
Fungal Proteins Hos2 protein, S pombe Saccharomyces cerevisiae Proteins Schizosaccharomyces pombe Proteins HST1 protein, S cerevisiae Set3 protein, S cerevisiae Sirtuin 2 Sirtuins Histone Deacetylases
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Pijnappel W W
Gene Expression Program, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Schaft D
Roguev A
Shevchenko A
Tekotte H
Wilm M
Rigaut G
Séraphin B
Aasland R
Stewart A F
References (63)
63 references, click to expand
  1. A role for histone deacetylase activity in HDAC1-mediated transcriptional repression.
    Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3519-24 PMID: 9520398
  2. The Groucho/transducin-like enhancer of split transcriptional repressors interact with the genetically defined amino-terminal silencing domain of histone H3.
    J Biol Chem. 1997 Oct 17;272(42):26604-10 PMID: 9334241
  3. The C-terminal SET domains of ALL-1 and TRITHORAX interact with the INI1 and SNR1 proteins, components of the SWI/SNF complex.
    Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4152-7 PMID: 9539705
  4. Beyond the nucleosome: epigenetic aspects of position-effect variegation in Drosophila.
    Cell. 1998 May 1;93(3):321-4 PMID: 9590165
  5. Polycombing the genome: PcG, trxG, and chromatin silencing.
    Cell. 1998 May 1;93(3):333-6 PMID: 9590168
  6. The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast.
    Nat Genet. 1998 Jun;19(2):192-5 PMID: 9620780
  7. WHSC1, a 90 kb SET domain-containing gene, expressed in early development and homologous to a Drosophila dysmorphy gene maps in the Wolf-Hirschhorn syndrome critical region and is fused to IgH in t(4;14) multiple myeloma.
    Hum Mol Genet. 1998 Jul;7(7):1071-82 PMID: 9618163
  8. Two distinct nuclear receptor interaction domains in NSD1, a novel SET protein that exhibits characteristics of both corepressors and coactivators.
    EMBO J. 1998 Jun 15;17(12):3398-412 PMID: 9628876
  9. Genomic disruption of six budding yeast genes gives one drastic example of phenotype strain-dependence.
    Yeast. 1998 May;14(7):655-64 PMID: 9639312
  10. Sif2p interacts with Sir4p amino-terminal domain and antagonizes telomeric silencing in yeast.
    Curr Biol. 1998 Jun 18;8(13):787-90 PMID: 9651685
  11. trithorax and the regulation of homeotic gene expression in Drosophila: a historical perspective.
    Int J Dev Biol. 1998;42(3):423-9 PMID: 9654027
  12. Gametogenesis in yeast is regulated by a transcriptional cascade dependent on Ndt80.
    Mol Cell. 1998 Apr;1(5):685-96 PMID: 9660952
  13. NDT80 and the meiotic recombination checkpoint regulate expression of middle sporulation-specific genes in Saccharomyces cerevisiae.
    Mol Cell Biol. 1998 Oct;18(10):5750-61 PMID: 9742092
  14. New constructs and strategies for efficient PCR-based gene manipulations in yeast.
    Yeast. 1998 Sep 15;14(12):1139-46 PMID: 9778799
  15. The transcriptional program of sporulation in budding yeast.
    Science. 1998 Oct 23;282(5389):699-705 PMID: 9784122
  16. Purification and biochemical properties of yeast SWI/SNF complex.
    Methods Enzymol. 1999;304:726-41 PMID: 10372393
  17. The ankyrin repeat: a diversity of interactions on a common structural framework.
    Trends Biochem Sci. 1999 Aug;24(8):311-6 PMID: 10431175
  18. A generic protein purification method for protein complex characterization and proteome exploration.
    Nat Biotechnol. 1999 Oct;17(10):1030-2 PMID: 10504710
  19. Protein folding: versatility of the cytosolic chaperonin TRiC/CCT.
    Curr Biol. 2000 Apr 6;10(7):R260-4 PMID: 10753735
  20. A core SMRT corepressor complex containing HDAC3 and TBL1, a WD40-repeat protein linked to deafness.
    Genes Dev. 2000 May 1;14(9):1048-57 PMID: 10809664
  21. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases.
    Proc Natl Acad Sci U S A. 2000 May 23;97(11):5807-11 PMID: 10811920
  22. A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family.
    Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6658-63 PMID: 10841563
  23. Cyclophilin A and Ess1 interact with and regulate silencing by the Sin3-Rpd3 histone deacetylase.
    EMBO J. 2000 Jul 17;19(14):3739-49 PMID: 10899127
  24. A strategy for the characterization of protein interaction networks by mass spectrometry.
    Biochem Soc Trans. 1999 Aug;27(4):549-54 PMID: 10917640
  25. Both corepressor proteins SMRT and N-CoR exist in large protein complexes containing HDAC3.
    EMBO J. 2000 Aug 15;19(16):4342-50 PMID: 10944117
  26. Regulation of chromatin structure by site-specific histone H3 methyltransferases.
    Nature. 2000 Aug 10;406(6796):593-9 PMID: 10949293
  27. The core meiotic transcriptome in budding yeasts.
    Nat Genet. 2000 Dec;26(4):415-23 PMID: 11101837
  28. The pachytene checkpoint in Saccharomyces cerevisiae requires the Sum1 transcriptional repressor.
    EMBO J. 2000 Dec 1;19(23):6489-97 PMID: 11101521
  29. Structure of the PHD zinc finger from human Williams-Beuren syndrome transcription factor.
    J Mol Biol. 2000 Dec 15;304(5):723-9 PMID: 11124022
  30. A biological atlas of functional maps.
    Cell. 2001 Feb 9;104(3):333-9 PMID: 11239391
  31. Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains.
    EMBO J. 2001 Jan 15;20(1-2):165-77 PMID: 11226167
  32. Skp1 forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly.
    Nat Cell Biol. 2001 Apr;3(4):384-91 PMID: 11283612
  33. A comprehensive two-hybrid analysis to explore the yeast protein interactome.
    Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-74 PMID: 11283351
  34. Conversion of a gene-specific repressor to a regional silencer.
    Genes Dev. 2001 Apr 15;15(8):955-67 PMID: 11316790
  35. NSD3, a new SET domain-containing gene, maps to 8p12 and is amplified in human breast cancer cell lines.
    Genomics. 2001 May 15;74(1):79-88 PMID: 11374904
  36. The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4.
    EMBO J. 2001 Dec 17;20(24):7137-48 PMID: 11742990
  37. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids.
    Anal Biochem. 1984 Apr;138(1):141-3 PMID: 6731838
  38. Positive control of sporulation-specific genes by the IME1 and IME2 products in Saccharomyces cerevisiae.
    Mol Cell Biol. 1990 May;10(5):2104-10 PMID: 2183020
  39. The Drosophila Polycomb-group gene Enhancer of zeste contains a region with sequence similarity to trithorax.
    Mol Cell Biol. 1993 Oct;13(10):6357-66 PMID: 8413234
  40. Parameters affecting lithium acetate-mediated transformation of Saccharomyces cerevisiae and development of a rapid and simplified procedure.
    Curr Genet. 1993 Nov;24(5):455-9 PMID: 8299163
  41. 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):3822-31 PMID: 7915232
  42. The PHD finger: implications for chromatin-mediated transcriptional regulation.
    Trends Biochem Sci. 1995 Feb;20(2):56-9 PMID: 7701562
  43. The Drosophila trithorax proteins contain a novel variant of the nuclear receptor type DNA binding domain and an ancient conserved motif found in other chromosomal proteins.
    Mech Dev. 1995 Aug;52(2-3):209-23 PMID: 8541210
  44. Altered Hox expression and segmental identity in Mll-mutant mice.
    Nature. 1995 Nov 30;378(6556):505-8 PMID: 7477409
  45. The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability.
    Genes Dev. 1995 Dec 1;9(23):2888-902 PMID: 7498786
  46. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p.
    Science. 1996 Apr 19;272(5260):408-11 PMID: 8602529
  47. Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4.
    Genes Dev. 1996 May 15;10(10):1247-59 PMID: 8675011
  48. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.
    Anal Chem. 1996 Mar 1;68(5):850-8 PMID: 8779443
  49. Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae.
    EMBO J. 1999 Nov 15;18(22):6448-54 PMID: 10562556
  50. Self-association of the SET domains of human ALL-1 and of Drosophila TRITHORAX and ASH1 proteins.
    Oncogene. 2000 Jan 20;19(3):351-7 PMID: 10656681
  51. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.
    Nature. 2000 Feb 10;403(6770):623-7 PMID: 10688190
  52. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase.
    Nature. 2000 Feb 17;403(6771):795-800 PMID: 10693811
  53. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
    Nucleic Acids Res. 1997 Dec 15;25(24):4876-82 PMID: 9396791
  54. SET1, a yeast member of the trithorax family, functions in transcriptional silencing and diverse cellular processes.
    Mol Biol Cell. 1997 Dec;8(12):2421-36 PMID: 9398665
  55. The Drosophila ash1 gene product, which is localized at specific sites on polytene chromosomes, contains a SET domain and a PHD finger.
    Genetics. 1996 Jun;143(2):913-28 PMID: 8725238
  56. The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB.
    Trends Biochem Sci. 1996 Mar;21(3):87-8 PMID: 8882580
  57. Mutations in the fission yeast silencing factors clr4+ and rik1+ disrupt the localisation of the chromo domain protein Swi6p and impair centromere function.
    J Cell Sci. 1996 Nov;109 ( Pt 11):2637-48 PMID: 8937982
  58. Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels.
    Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14440-5 PMID: 8962070
  59. 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):14503-8 PMID: 8962081
  60. Functional dissection of the B" component of RNA polymerase III transcription factor IIIB: a scaffolding protein with multiple roles in assembly and initiation of transcription.
    Mol Cell Biol. 1997 Apr;17(4):1868-80 PMID: 9121435
  61. Flow cytometric analysis of DNA content in budding yeast.
    Methods Enzymol. 1997;283:322-32 PMID: 9251030
  62. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  63. Association of SET domain and myotubularin-related proteins modulates growth control.
    Nat Genet. 1998 Apr;18(4):331-7 PMID: 9537414
Article Info
Journal
Genes & development
Abbr.
Genes Dev
ISSN
0890-9369
DOI
10.1101/gad.207401
Published
2001-11-15
Pages
2991-3004
Language
English
Region
United States
NLM ID
8711660
PMCID
PMC312828
Subset
IM
External Links
PubMed source DOI: 10.1101/gad.207401 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2