The Rpd3 Core Complex Is a Chromatin Stabilization Module

Chen, Xiao Fen; Kuryan, Benjamin G.; Kitada, Tasuku; Tran, Nancy; Li, Jing Yu; Kurdistani, Siavash K.; Grunstein, Michael; Li, Bing; Carey, Michael

doi:10.1016/j.cub.2011.11.042

Cited by 49 publications

(53 citation statements)

References 40 publications

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“…Several possible interpretations of this result are addressed in the Discussion, but the lack of major acetylation changes could indicate that Rpd3 has an alternative function in nucleosome deposition at the rDNA independent of its role as a histone deacetylase. Indeed, a core Rpd3 complex was recently shown to have nucleosome assembly activity in vitro, similar to histone chaperones such as Asf1, Spt6, and FACT (37).…”

Section: Resultsmentioning

confidence: 99%

Rpd3- and Spt16-Mediated Nucleosome Assembly and Transcriptional Regulation on Yeast Ribosomal DNA Genes

Johnson

French

Osheim

et al. 2013

Molecular and Cellular Biology

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Ribosomal DNA (rDNA) genes in eukaryotes are organized into multicopy tandem arrays and transcribed by RNA polymerase I. During cell proliferation, ϳ50% of these genes are active and have a relatively open chromatin structure characterized by elevated accessibility to psoralen cross-linking. In Saccharomyces cerevisiae, transcription of rDNA genes becomes repressed and chromatin structure closes when cells enter the diauxic shift and growth dramatically slows. In this study, we found that nucleosomes are massively depleted from the active rDNA genes during log phase and reassembled during the diauxic shift, largely accounting for the differences in psoralen accessibility between active and inactive genes. The Rpd3L histone deacetylase complex was required for diauxic shift-induced H4 and H2B deposition onto rDNA genes, suggesting involvement in assembly or stabilization of the entire nucleosome. The Spt16 subunit of FACT, however, was specifically required for H2B deposition, suggesting specificity for the H2A/H2B dimer. Miller chromatin spreads were used for electron microscopic visualization of rDNA genes in an spt16 mutant, which was found to be deficient in the assembly of normal nucleosomes on inactive genes and the disruption of nucleosomes on active genes, consistent with an inability to fully reactivate polymerase I (Pol I) transcription when cells exit stationary phase.

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Section: Resultsmentioning

confidence: 99%

Rpd3- and Spt16-Mediated Nucleosome Assembly and Transcriptional Regulation on Yeast Ribosomal DNA Genes

Johnson

French

Osheim

et al. 2013

Molecular and Cellular Biology

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“…Present in fungi, protozoa, and plants, but not in animals and humans, Rxt3/HDC1 homologs are potentially interesting targets for drug and crop development, but their role in non-plant species has remained obscure. In yeast, Rxt3 coelutes with other proteins of the large Rpd3 histone deacetylation complex, but the protein is neither required for deacetylation of known Rpd3 targets nor for in vitro reassembly of a minimal functional Rpd3 complex (Carrozza et al, 2005a;Chen et al, 2012). The protein sequence of Rxt3 does not contain any regions with known function in enzymatic activity or histone/DNA binding properties.…”

Section: Discussion Plant Hdc1-type Proteins Have Extended From Smallmentioning

confidence: 99%

“…To enable these processes, HDACs interact with other proteins that establish a structural link between the core deacetylation enzymes, the histones, and the DNA. Several such multiprotein complexes have been biochemically purified in yeast and mammalian cells (Carrozza et al, 2005a(Carrozza et al, , 2005bRoguev and Krogan, 2007;Yang and Seto, 2008;Chen et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Histone Deacetylase Complex1 Expression Level Titrates Plant Growth and Abscisic Acid Sensitivity in Arabidopsis

et al. 2013

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Histone deacetylation regulates gene expression during plant stress responses and is therefore an interesting target for epigenetic manipulation of stress sensitivity in plants. Unfortunately, overexpression of the core enzymes (histone deacetylases [HDACs]) has either been ineffective or has caused pleiotropic morphological abnormalities. In yeast and mammals, HDACs operate within multiprotein complexes. Searching for putative components of plant HDAC complexes, we identified a gene with partial homology to a functionally uncharacterized member of the yeast complex, which we called Histone Deacetylation Complex1 (HDC1). HDC1 is encoded by a single-copy gene in the genomes of model plants and crops and therefore presents an attractive target for biotechnology. Here, we present a functional characterization of HDC1 in Arabidopsis thaliana. We show that HDC1 is a ubiquitously expressed nuclear protein that interacts with at least two deacetylases (HDA6 and HDA19), promotes histone deacetylation, and attenuates derepression of genes under water stress. The fast-growing HDC1-overexpressing plants outperformed wild-type plants not only on well-watered soil but also when water supply was reduced. Our findings identify HDC1 as a rate-limiting component of the histone deacetylation machinery and as an attractive tool for increasing germination rate and biomass production of plants.

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“…1B, lane 2); (ii) Sin3, Rpd3, and Ume1 form the Rpd3 core complex (Fig. 1C) (42), which is shared between Rpd3S and Rpd3L (29); and (iii) without Ume1 (Fig. 1C, lane 1) or Rpd3 (Fig.…”

Section: Rpd3s Contains Two Copies Of Rco1 As Revealed By Subunitintementioning

confidence: 99%

Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex

Ruan

Cui

Lee

et al. 2016

Journal of Biological Chemistry

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Recognition of histone post-translational modifications is pivotal for directing chromatin-modifying enzymes to specific genomic regions and regulating their activities. Emerging evidence suggests that other structural features of nucleosomes also contribute to precise targeting of downstream chromatin complexes, such as linker DNA, the histone globular domain, and nucleosome spacing. However, how chromatin complexes coordinate individual interactions to achieve high affinity and specificity remains unclear. The Rpd3S histone deacetylase utilizes the chromodomain-containing Eaf3 subunit and the PHD domain-containing Rco1 subunit to recognize nucleosomes that are methylated at lysine 36 of histone H3 (H3K36me). We showed previously that the binding of Eaf3 to H3K36me can be allosterically activated by Rco1. To investigate how this chromatin recognition module is regulated in the context of the Rpd3S complex, we first determined the subunit interaction network of Rpd3S. Interestingly, we found that Rpd3S contains two copies of the essential subunit Rco1, and both copies of Rco1 are required for full functionality of Rpd3S. Our functional dissection of Rco1 revealed that besides its known chromatin-recognition interfaces, other regions of Rco1 are also critical for Rpd3S to recognize its nucleosomal substrates and function in vivo. This unexpected result uncovered an important and understudied aspect of chromatin recognition. It suggests that precisely reading modified chromatin may not only need the combined actions of reader domains but also require an internal signaling circuit that coordinates the individual actions in a productive way.It is now widely accepted that histone post-translational modifications (PTMs) 2 and other structural features of chromatin, such as variant histones and DNA modifications, mainly serve as signal platforms to direct downstream regulatory events (1, 2). In general, four major components of chromatin structure contribute to the signals that can be interpreted by downstream chromatin regulators. (i) Histone peptides that carry certain PTMs contribute. Specifically modified histone peptides can be recognized by protein domains/motifs that are commonly referred as PTM "readers." A large repertoire of such domain/PTM interactions have been documented, and they are essential for targeting downstream factors to a given genomic locus (3). Reader domains not only distinguish different types of modifications and the locations of PTMs but also the specific states of modifications. However, due to relatively weak affinity, it is unclear whether these interactions are sufficient to mediate the recruitment of chromatin complexes. For example, although histone H3 methylation at residue Lys-36 (H3K36me) is an essential signal for the histone deacetylase Rpd3S, the contact between the chromodomain of the Eaf3 subunit (CHD Eaf3 ) of Rpd3S and H3K366me only contributes to the binding specificity but not to the overall affinity (4). (ii) Histone globular domains contribute. Because PTMs are mostly cl...

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The Rpd3 Core Complex Is a Chromatin Stabilization Module

Cited by 49 publications

References 40 publications

Rpd3- and Spt16-Mediated Nucleosome Assembly and Transcriptional Regulation on Yeast Ribosomal DNA Genes

Rpd3- and Spt16-Mediated Nucleosome Assembly and Transcriptional Regulation on Yeast Ribosomal DNA Genes

Histone Deacetylase Complex1 Expression Level Titrates Plant Growth and Abscisic Acid Sensitivity in Arabidopsis

Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex

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