The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast

Rubertis, Francesco De; Kadosh, David; Henchoz, Sandra; Pauli, Daniel; Reuter, Günter; Struhl, Kevin; Spierer, Pierre

doi:10.1038/384589a0

Cited by 217 publications

(159 citation statements)

References 26 publications

Supporting

Mentioning

151

Contrasting

Unclassified

Order By: Relevance

“…In yeast, acetylation of particular lysines in the H4 N-terminal tail region appears to be required for silencing (Braunstein et al, 1996). In addition, knockout of the HDAC-encoding Rpd3 gene leads to increased genomic silencing in yeast and Drosophila (De Rubertis 1996;Rundlett et al, 1996) and yeast strains carrying deletions of Rpd3 fail to show proper activation of particular genes Rundlett et al, 1996). Histones at some yeast gene promoters have been shown to become deacetylated upon activation of the promoter (Deckert and Struhl, 2001), and in mammalian cells, some genes are repressed by HDAC inhibitors.…”

Section: Introductionmentioning

confidence: 99%

Inhibition of MMTV transcription by HDAC inhibitors occurs independent of changes in chromatin remodeling and increased histone acetylation

2003

View full text Add to dashboard Cite

Increased histone acetylation has been associated with activated gene transcription and decreased acetylation with repression. However, there is a growing number of genes known, which are downregulated by histone deacetylase (HDAC) inhibitors through unknown mechanisms. This study examines the mechanism by which the mouse mammary tumor virus (MMTV) promoter is repressed by the HDAC inhibitor, trichostatin A (TSA). We find that this repression is transcriptional in nature and that it occurs in the presence and absence of glucocorticoids. TSA decreases MMTV transcription at a rapid rate, reaching maximum in 30-60 min. In contrast with previous reports, the repression does not correlate with an inhibition of glucocorticoid-induced nuclease hypersensitivity or NF1-binding at the MMTV promoter. Surprisingly, TSA does not induce sizable increases in histone acetylation at the MMTV promoter nor does it inhibit histone deacetylation, which accompanies deactivation of the glucocorticoid-activated MMTV promoter. Repression of MMTV transcription by TSA does not depend on the chromatin organization of the promoter because a transiently transfected MMTV promoter construct with a disorganized nucleoprotein structure was also repressed by TSA treatment. Mutational analysis of the MMTV promoter indicates that repression by TSA is mediated through the TATA box region. These results suggest a novel mechanism that involves acetylation of nonhistone proteins necessary for basal transcription.

show abstract

Section: Introductionmentioning

confidence: 99%

Inhibition of MMTV transcription by HDAC inhibitors occurs independent of changes in chromatin remodeling and increased histone acetylation

2003

View full text Add to dashboard Cite

show abstract

“…As more is learned about the enzymes catalyzing these modifications, the histone acetyltransferases (HATs) and histone deacetylases (HDACs), simple functional distinctions between acetylation and deacetylation of histones do not hold (Iizuka and Smith, 2003). For example, in several organisms, mutations in RPD3, a gene encoding a deacetylase, lead to increases in silencing rather than the expected decreases (DeRubertis et al, 1996;Rundlett et al, 1996). This brings forward the possibility that histone acetylation may play an important part in both silent and active chromatin.…”

mentioning

confidence: 99%

Distinct Roles for the Essential MYST Family HAT Esa1p in Transcriptional Silencing

Clarke

Samal

Pillus

2006

MBoC

View full text Add to dashboard Cite

Among acetyltransferases, the MYST family enzyme Esa1p is distinguished for its essential function and contribution to transcriptional activation and DNA double-stranded break repair. Here we report that Esa1p also plays a key role in silencing RNA polymerase II (Pol II)-transcribed genes at telomeres and within the ribosomal DNA (rDNA) of the nucleolus. These effects are mediated through Esa1p's HAT activity and correlate with changes within the nucleolus. Esa1p is enriched within the rDNA, as is the NAD-dependent protein deacetylase Sir2p, and the acetylation levels of key Esa1p histone targets are reduced in the rDNA in esa1 mutants. Although mutants of both ESA1 and SIR2 have enhanced rates of rDNA recombination, esa1 effects are more modest yet result in distinct structural changes of rDNA chromatin. Surprisingly, increased expression of ESA1 can bypass the requirement for Sir2p in rDNA silencing, suggesting that these two enzymes with seemingly opposing activities both contribute to achieve optimal nucleolar chromatin structure and function. INTRODUCTIONHistone modifications such as phosphorylation, methylation, acetylation, and deacetylation provide a mechanism by which chromatin structure is modulated to affect gene expression both positively and negatively (for reviews see Strahl and Allis, 2000;Iizuka and Smith, 2003;Kurdistani and Grunstein, 2003). The acetylation of lysine residues on histone N-terminal tails is classically linked to increases in gene expression and more directly to roles in transcriptional activation. By contrast, deacetylation of histones is most frequently correlated with transcriptionally silent chromatin. As more is learned about the enzymes catalyzing these modifications, the histone acetyltransferases (HATs) and histone deacetylases (HDACs), simple functional distinctions between acetylation and deacetylation of histones do not hold (Iizuka and Smith, 2003). For example, in several organisms, mutations in RPD3, a gene encoding a deacetylase, lead to increases in silencing rather than the expected decreases (DeRubertis et al., 1996;Rundlett et al., 1996). This brings forward the possibility that histone acetylation may play an important part in both silent and active chromatin. In addition, coactivator proteins, such as the histone acetyltransferases p300 and CBP and nuclear hormone receptors, appear to have roles in transcriptional repression through acetylation and association with particular binding partners (for examples, see Chen and Li, 1998;Waltzer and Bienz, 1998;Baluchamy et al., 2003;Girdwood et al., 2003;Rajabi et al., 2005). Thus, understanding of multiple roles for acetylation in controlling gene expression is expanding.In Saccharomyces cerevisiae, there are three regions of the genome controlled by chromatin-mediated transcriptional silencing: telomeres, the silent mating-type loci HMR and HML, and the rDNA array. Many factors are important for transcriptional silencing at subsets of these loci including the four core histones, the repressor activator protein Rap1...

show abstract

“…Besides human and mouse, highly homologous yeast RPD3 sequences have been identified in Drosophila (21), Caenorhabditis elegans (X78454 and 1176665), and Xenopus laevis (gi:576995). Currently, it has not yet been established whether the C. elegans or X. laevis RPD3-related proteins have histone deacetylase activities or whether they play a role in transcriptional repression.…”

mentioning

confidence: 99%

Isolation and Characterization of cDNAs Corresponding to an Additional Member of the Human Histone Deacetylase Gene Family

Yang

Yao

Sun

et al. 1997

Journal of Biological Chemistry

401

301

View full text Add to dashboard Cite

Several human cDNAs encoding a histone deacetylase protein, HDAC3, have been isolated. Analysis of the predicted amino acid sequence of HDAC3 revealed an open reading frame of 428 amino acids with a predicted molecular mass of 49 kDa. The HDAC3 protein is 50% identical in DNA sequence and 53% identical in protein sequence compared with the previously cloned human HDAC1. Comparison of the HDAC3 sequence with human HDAC2 also yielded similar results, with 51% identity in DNA sequence and 52% identity in protein sequence. The expressed HDAC3 protein is functionally active because it possesses histone deacetylase activity, represses transcription when tethered to a promoter, and binds transcription factor YY1. Similar to HDAC1 and HDAC2, HDAC3 is ubiquitously expressed in many different cell types.The organization of chromatin structure is a fundamental and significant component of transcriptional regulation in all eukaryotic cells. Transcriptionally active or repressed chromatin is determined, at least in part, by the modification of histones. For example, hyperacetylation of histones generally leads to an increase in transcription, whereas hypoacetylation of histones appears to have the opposite effect (reviewed in Refs. 1-4). Nuclear histone acetyltransferases such as transcription factors GCN5, PCAF, p300/CBP, and TAF II 230/250 have been identified from different organisms (5-9).Several yeast and mammalian histone deacetylases have been identified, and their corresponding genes have been cloned (10 -12). In yeast, the HDA1 protein, which shares sequence similarity to RPD3, is a subunit of a large histone deacetylase complex HDA. RPD3 is also associated with another yeast histone deacetylase complex HDB. Using a trapoxin (an inhibitor of histone deacetylase) affinity matrix, Taunton et al. (10) purified and cloned a human 55-kDa protein related to the yeast protein RPD3. Immunoprecipitation of this 55-kDa protein, HDAC1 (also called HD1), showed that it contains histone deacetylase activity. A second human histone deacetylase protein, HDAC2, with high homology to yeast RPD3 was identified based on a yeast two-hybrid trap experiment with the YY1 transcription factor as a bait (11). YY1 negatively regulates transcription by tethering HDAC2 to DNA as a corepressor. Both HDAC1 and HDAC2 exist in a complex with the corepressor mSIN3 and mediate Mad transcriptional repression (13-15). In addition, HDAC1 and HDAC2 are essential components of two thyroid hormone receptor corepressors, N-CoR and SMRT (16 -18). HDAC1 is also an important factor that represses transactivation by progesterone receptor (19).The yeast RPD3 protein was originally identified in genetic screens for transcriptional repressors (20). Besides human and mouse, highly homologous yeast RPD3 sequences have been identified in Drosophila (21), Caenorhabditis elegans (X78454 and 1176665), and Xenopus laevis (gi:576995). Currently, it has not yet been established whether the C. elegans or X. laevis RPD3-related proteins have histone deacetylase activities o...

show abstract

The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast

Cited by 217 publications

References 26 publications

Inhibition of MMTV transcription by HDAC inhibitors occurs independent of changes in chromatin remodeling and increased histone acetylation

Inhibition of MMTV transcription by HDAC inhibitors occurs independent of changes in chromatin remodeling and increased histone acetylation

Distinct Roles for the Essential MYST Family HAT Esa1p in Transcriptional Silencing

Isolation and Characterization of cDNAs Corresponding to an Additional Member of the Human Histone Deacetylase Gene Family

Contact Info

Product

Resources

About