| Structural highlights
Function
RPD3_YEAST Catalytic component of the RPD3 histone deacetylase (HDAC) complexes RPD3C(L) and RPD3C(S) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation plays an important role in transcriptional regulation, cell cycle progression, DNA damage response, osmotic stress response and developmental events. Is involved in rDNA and telomere silencing and in double strand breaks repair. Required for both full transcription repression and activation of many genes including cell type-specific genes (STE6, TY2 and HO), cell differentiation-specific genes (SPO13), genes that respond to external signals (PHO5) and TRK2. The RPD3 complexes regulate also chromosomal replication timing.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19]
Publication Abstract from PubMed
The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron microscopy structures of the budding yeast Rpd3S complex in both its apo and three nucleosome-bound states at atomic resolutions, revealing the exquisite architecture of Rpd3S to well accommodate a mononucleosome without linker DNA. The Rpd3S core, containing a Sin3 Lobe and two NB modules, is a rigid complex and provides three positive-charged anchors (Sin3_HCR and two Rco1_NIDs) to connect nucleosomal DNA. In three nucleosome-bound states, the Rpd3S core exhibits three distinct orientations relative to the nucleosome, assisting the sector-shaped deacetylase Rpd3 to locate above the SHL5-6, SHL0-1, or SHL2-3, respectively. Our work provides a structural framework that reveals a dynamic working model for the Rpd3S complex to engage diverse deacetylation sites.
Structures and dynamics of Rpd3S complex bound to nucleosome.,Wang C, Chu C, Guo Z, Zhan X Sci Adv. 2024 Apr 12;10(15):eadk7678. doi: 10.1126/sciadv.adk7678. Epub 2024 Apr , 10. PMID:38598631[20]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
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- ↑ Burgess SM, Ajimura M, Kleckner N. GCN5-dependent histone H3 acetylation and RPD3-dependent histone H4 deacetylation have distinct, opposing effects on IME2 transcription, during meiosis and during vegetative growth, in budding yeast. Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):6835-40. PMID:10359799 doi:10.1073/pnas.96.12.6835
- ↑ Sun ZW, Hampsey M. A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics. 1999 Jul;152(3):921-32. PMID:10388812 doi:10.1093/genetics/152.3.921
- ↑ Elkhaimi M, Kaadige MR, Kamath D, Jackson JC, Biliran H Jr, Lopes JM. Combinatorial regulation of phospholipid biosynthetic gene expression by the UME6, SIN3 and RPD3 genes. Nucleic Acids Res. 2000 Aug 15;28(16):3160-7. PMID:10931932 doi:10.1093/nar/28.16.3160
- ↑ Watson AD, Edmondson DG, Bone JR, Mukai Y, Yu Y, Du W, Stillman DJ, Roth SY. Ssn6-Tup1 interacts with class I histone deacetylases required for repression. Genes Dev. 2000 Nov 1;14(21):2737-44. PMID:11069890
- ↑ Kurdistani SK, Robyr D, Tavazoie S, Grunstein M. Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet. 2002 Jul;31(3):248-54. PMID:12089521 doi:10.1038/ng907
- ↑ Deckert J, Struhl K. Targeted recruitment of Rpd3 histone deacetylase represses transcription by inhibiting recruitment of Swi/Snf, SAGA, and TATA binding protein. Mol Cell Biol. 2002 Sep;22(18):6458-70. PMID:12192044 doi:10.1128/MCB.22.18.6458-6470.2002
- ↑ Scott KL, Plon SE. Loss of Sin3/Rpd3 histone deacetylase restores the DNA damage response in checkpoint-deficient strains of Saccharomyces cerevisiae. Mol Cell Biol. 2003 Jul;23(13):4522-31. PMID:12808094 doi:10.1128/MCB.23.13.4522-4531.2003
- ↑ Jazayeri A, McAinsh AD, Jackson SP. Saccharomyces cerevisiae Sin3p facilitates DNA double-strand break repair. Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1644-9. PMID:14711989 doi:10.1073/pnas.0304797101
- ↑ De Nadal E, Zapater M, Alepuz PM, Sumoy L, Mas G, Posas F. The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. Nature. 2004 Jan 22;427(6972):370-4. PMID:14737171 doi:10.1038/nature02258
- ↑ Schröder M, Clark R, Liu CY, Kaufman RJ. The unfolded protein response represses differentiation through the RPD3-SIN3 histone deacetylase. EMBO J. 2004 Jun 2;23(11):2281-92. PMID:15141165 doi:10.1038/sj.emboj.7600233
- ↑ Aparicio JG, Viggiani CJ, Gibson DG, Aparicio OM. The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae. Mol Cell Biol. 2004 Jun;24(11):4769-80. PMID:15143171 doi:10.1128/MCB.24.11.4769-4780.2004
- ↑ Sabet N, Volo S, Yu C, Madigan JP, Morse RH. Genome-wide analysis of the relationship between transcriptional regulation by Rpd3p and the histone H3 and H4 amino termini in budding yeast. Mol Cell Biol. 2004 Oct;24(20):8823-33. PMID:15456858 doi:10.1128/MCB.24.20.8823-8833.2004
- ↑ Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell. 2005 Nov 18;123(4):593-605. PMID:16286008 doi:10.1016/j.cell.2005.10.025
- ↑ Vidal M, Gaber RF. RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae. Mol Cell Biol. 1991 Dec;11(12):6317-27. PMID:1944291 doi:10.1128/mcb.11.12.6317-6327.1991
- ↑ Rundlett SE, Carmen AA, Kobayashi R, Bavykin S, Turner BM, 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):14503-8. PMID:8962081 doi:10.1073/pnas.93.25.14503
- ↑ 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):1343-53. PMID:8978024 doi:10.1093/genetics/144.4.1343
- ↑ 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. PMID:9512514 doi:10.1101/gad.12.6.797
- ↑ 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):5121-7. PMID:9710596 doi:10.1128/MCB.18.9.5121
- ↑ Wang C, Chu C, Guo Z, Zhan X. Structures and dynamics of Rpd3S complex bound to nucleosome. Sci Adv. 2024 Apr 12;10(15):eadk7678. PMID:38598631 doi:10.1126/sciadv.adk7678
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