Evolutionary origin of histone deacetylases

Searches of several sequence databases reveal that human HD1, yeast HDA1, yeast RPD3 and other eukaryotic histone deacetylases share nine motifs with archaeal and eubacterial enzymes, including acetoin utilization protein (acuC) and acetylpolyamine amidohydrolase. Histone deacetylase and acetylpolyamine amidohydrolase also share profound functional similarities. Both of them (1) recognize an acetylated aminoalkyl group; (2) catalyze the removal of the acetyl group by cleaving an amide bond, and (3) increase the positive charge of the substrate. Stabilization of nucleosomal DNA-histone interaction brought about by the change in charge has been implicated as the underlying cause for histone deacetylase-mediated transcriptional repression. It is speculated that the eukaryotic histone deacetylases originated from a prokaryotic enzyme similar to the acetylpolyamine amidohydrolases that relied on reversible acetylation and deacetylation of the aminoalkyl group of a DNA binding molecule to achieve a gene regulatory effect (Leipe, 1997).

Drosophila histone deacetylases

The steady-state level of histone acetylation in eukaryotes is established and maintained by multiple histone acetyltransferases (HATs) and histone deacetylases (HDACs) and affects both the structure and the function of chromatin. Histone deacetylases play a key role in the regulation of transcription, and form a highly conserved protein family in many eukaryotic species. The cloning, sequencing and genetic mapping is described for two histone deacetylase genes in Drosophila: dHDAC1 is essentially identical to the previously cloned D. melanogaster d-Rpd3 gene and dHDAC3, a novel gene, is orthologous to the human and the chicken (Gallus gallus) HDAC3 genes. The predicted amino acid sequence (438 aa) of dHDAC3 shows 58.1% identity with dHDAC1/d-Rpd3, the only previously known member of the HDAC family in this organism. The map positions on polytene chromosomes for dHDAC1 and dHDAC3 were determined as 64C1-6 and 83A3-4 respectively. A search for other dHDAC3-like genes failed to find other potential paralogs in D. melanogaster, but identified significant homologies with bacterial and fungal genes encoding enzymes that metabolize acetyl groups, and with genes for other hydrolyases such as carboxypeptidase. In addition, histone deacetylase activity in D. melanogaster nuclear extracts can be inhibited by high concentrations of zinc and activated by low concentrations, which is identical to the properties of bovine carboxypeptidase A. On the basis of sequence and functional similarities, it is suggested that histone deacetylases are metal-substituted enzymes (Johnson, 1998).

Yeast histone deacetylases

The SIN3 gene is required for the transcriptional repression of diverse genes in Saccharomyces cerevisiae. Sin3p does not bind directly to DNA but is thought to be targeted to promoters by interacting with sequence-specific DNA-binding proteins. Sin3p is shown to be present in a large multiprotein complex with an apparent molecular mass, estimated by gel filtration chromatography, of greater than 2 million Da. Genetic studies have shown that the yeast RPD3 gene has a function similar to that of SIN3 in transcriptional regulation, since SIN3 and RPD3 negatively regulate the same set of genes. The SIN3 and RPD3 genes are conserved from yeasts to mammals, and recent work suggests that RPD3 may encode a histone deacetylase. Rpd3p is shown to be present in the Sin3p complex and an rpd3 mutation is shown to eliminate SIN3-dependent repression. Thus, Sin3p may function as a bridge to recruit the Rpd3p histone deacetylase to specific promoters (Kasten, 1997).

Increased histone acetylation has been correlated with increased transcription, and regions of heterochromatin are generally hypoacetylated. In investigating the cause-and-effect relationship between histone acetylation and gene activity, two yeast histone deacetylase complexes have been characterized. Histone deacetylase-A (HDA) is an approximately 350-kDa complex that is highly sensitive to the deacetylase inhibitor trichostatin A. Histone deacetylase-B (HDB) is an approximately 600-kDa complex that is much less sensitive to trichostatin A. The HDA1 protein (a subunit of the HDA activity) shares sequence similarity to RPD3, a factor required for optimal transcription of certain yeast genes. RPD3 is associated with the HDB activity. HDA1 also shares similarity to three new open reading frames in yeast, designated HOS1, HOS2, and HOS3. Both hda1 and rpd3 deletions increase acetylation levels in vivo at all sites examined in both core histones H3 and H4, with rpd3 deletions having a greater impact on histone H4 lysine positions 5 and 12. Surprisingly, both hda1 and rpd3 deletions increase repression at telomeric loci, which resemble heterochromatin, with rpd3 having a greater effect. In addition, rpd3 deletions retard full induction of the PHO5 promoter fused to the reporter lacZ. These data demonstrate that the histone acetylation state has a role in regulating both heterochromatic silencing and regulated gene expression (Rundlett, 1996).

hda1+ (histone deacetylase 1) is a fission yeast gene that is highly similar in sequence to known histone deacetylase genes in humans and budding yeast. This putative histone deacetylase contributes to transcriptional silencing in the fission yeast Schizosaccharomyces pombe. A precise deletion allele of the hda1+ open reading frame was created. Cells lacking the hda1+ gene are viable. However, genetic analysis reveals that cells without hda1 + display enhanced gene repression/silencing of marker genes, residing adjacent to telomeres, close to the silent mating-type loci and within centromere I. This phenotype is very similar to that recently reported for rpd3 mutants both in Drosophila and budding yeast. No defects in chromosome segregation or changes in telomere length have been detected. Cells lacking the hda1+ gene display reduced sporulation. Growth of hda1 cells is partially inhibited by low concentrations of Trichostatin A (TSA), a known inhibitor of histone deacetylase enzymes. TSA treatment is also able to overcome the enhanced silencing found in heterochromatic regions of hda1 cells. These results indicate a genetic redundancy with respect to deacetylase genes and partially overlapping functions of these genes in fission yeast (Olsson, 1998).

Post-translational modification of histones enables dynamic regulation of chromatin structure in eukaryotes. Histone acetyltransferase (HAT) and histone deacetylase (HDAC) modify the N-terminal tails of histones by adding or removing acetyl groups to specific lysine residues. A particular pair of HAT (Esa1) and HDAC (Rpd3) is proposed to modify the same lysine residue in vitro and in vivo. Thus, HAT and HDAC might have similar structural and functional motifs. HAT (Esa1 family) and HDAC (Rpd3 family) have similar amino acid stretches in the primary structures through evolution. This region is referred to as the 'ER (Esa1-Rpd3) motif'. In the tertiary structure of Esa1, the ER motif is located near the active center. In Rpd3, for which the tertiary structure remains unclear, the ER motif contains the same secondary structure as found in Esa1 as seen by circular dichroism analysis. Alanine-scanning mutagenesis was performed; the ER motif regions of Esa1 or Rpd3 were found to be required for HAT activity of Esa1 or HDAC activity of Rpd3, respectively. The discovery of the ER motif present in the pair of enzymes (HAT and HDAC) indicates that HAT and HDAC have common structural bases, although they catalyze the reaction with opposite functions (Adachi, 2002).

The presence of Set2-mediated methylation of H3K36 (K36me; see Drosophila Set2) correlates with transcription frequency throughout the yeast genome. K36me targets the Rpd3S complex to deacetylate transcribed regions and suppress cryptic transcription initiation at certain genes. Using a genome-wide approach, this study reports that the Set2-Rpd3S pathway is generally required for controlling acetylation at coding regions. When using acetylation as a functional readout for this pathway, longer genes and, surprisingly, genes transcribed at lower frequency exhibit a stronger dependency. Moreover, a systematic screen using high-resolution tiling microarrays allowed identification of a group of genes that rely on Set2-Rpd3S to suppress spurious transcripts. Interestingly, most of these genes are within the group that depend on the same pathway to maintain a hypoacetylated state at coding regions. These data highlight the importance of using the functional readout of histone codes to define the roles of specific pathways (Li, 2007).

Heterochromatin plays a key role in protection of chromosome integrity by suppressing homologous recombination. In Saccharomyces cerevisiae, Sir2p, Sir3p, and Sir4p are structural components of heterochromatin found at telomeres and the silent mating-type loci. This study investigated whether incorporation of Sir proteins into minichromosomes regulates early steps of recombinational repair in vitro. It was found that addition of Sir3p to a nucleosomal substrate is sufficient to eliminate yRad51p-catalyzed formation of joints, and that this repression is enhanced by Sir2p/Sir4p. Importantly, Sir-mediated repression requires histone residues that are critical for silencing in vivo. Moreover, the SWI/SNF chromatin-remodeling enzyme facilitates joint formation by evicting Sir3p, thereby promoting subsequent Rad54p-dependent formation of a strand invasion product. These results suggest that recombinational repair in the context of heterochromatin presents additional constraints that can be overcome by ATP-dependent chromatin-remodeling enzymes (Sinha, 2009).

Signaling upstream of yeast histone deacetylases

Ume1p is a member of a conserved protein family including RbAp48 that associates with histone deacetylases. Consistent with this finding, Ume1p is required for the full repression of a subset of meiotic genes during vegetative growth in budding yeast. In addition to mitotic cell division, this report describes a new role for Ume1p in meiotic gene repression in precommitment sporulating cultures returning to vegetative growth. However, Ume1p is not required to re-establish repression as part of the meiotic transient transcription program. Mutational analysis has revealed that two conserved domains (NEE box and a WD repeat motif) are required for Ume1p-dependent repression. Co-immunoprecipitation studies reveal that both the NEE box and the WD repeat motif are essential for normal Rpd3p binding. Finally, Ume1p-Rpd3p association is dependent on the global co-repressor Sin3p. Moreover, this activity was localized to one of the four paired amphipathic-helix domains of Sin3p shown previously to be required for transcriptional repression. These findings support a model that Ume1p binding to Rpd3p is required for its repression activity. In addition, these results suggest that Rpd3-Ume1p-Sin3p comprises an interdependent complex required for mediating transcriptional repression (Mallory, 2003).

The Tup1-Ssn6 corepressor complex in Saccharomyces cerevisiae represses the transcription of a diverse set of genes. Chromatin is an important component of Tup1-Ssn6-mediated repression. Tup1 binds to underacetylated histone tails and requires multiple histone deacetylases (HDACs) for its repressive functions. Physical interactions of the corepressor complex with the class I HDACs Rpd3, Hos2, and Hos1, are described in this study. In contrast, no in vivo interaction was observed between Tup-Ssn6 and Hda1, a class II HDAC. Rpd3 interacts with both Tup1 and Ssn6. Rpd3 and Hos2 interact with Ssn6 independently of Tup1 via distinct tetratricopeptide domains within Ssn6, suggesting that these two HDACs may contact the corepressor at the same time (Davie, 2003).

Regulation of gene expression by mitogen-activated protein kinases (MAPKs) is essential for proper cell adaptation to extracellular stimuli. Exposure of yeast cells to high osmolarity results in rapid activation of the MAPK Hog1, which coordinates the transcriptional program required for cell survival on osmostress. The mechanisms by which Hog1 and MAPKs in general regulate gene expression are not completely understood, although Hog1 can modify some transcription factors. It is proposed that Hog1 induces gene expression by a mechanism that involves recruiting a specific histone deacetylase complex to the promoters of genes regulated by osmostress. Cells lacking the Rpd3-Sin3 histone deacetylase complex are sensitive to high osmolarity and show compromised expression of osmostress genes. Hog1 interacts physically with Rpd3 in vivo and in vitro and, on stress, targets the deacetylase to specific osmostress-responsive genes. Binding of the Rpd3-Sin3 complex to specific promoters leads to histone deacetylation, entry of RNA polymerase II and induction of gene expression. Together, these data indicate that targeting of the Rpd3 histone deacetylase to osmoresponsive promoters by the MAPK Hog1 is required to induce gene expression on stress (De Nadal, 2004).

Yeast histone deacetylases are found in protein complexes

Histone acetylation and deacetylation are catalyzed by structurally distinct, multisubunit complexes that mediate, respectively, activation and repression of transcription. SAP30 has been identified as a novel component of the human histone deacetylase complex that includes Sin3, the histone deacetylases HDAC1 and HDAC2, histone binding proteins RbAp46 and RbAp48, as well as other polypeptides. A SAP30 homolog is described in yeast that is functionally related to Sin3 and the histone deacetylase Rpd3. The human SAP30 complex is active in deacetylating core histone octamers, but inactive in deacetylating nucleosomal histones due to the inability of the histone binding proteins RbAp46 and RbAp48 to gain access to nucleosomal histones. These results define SAP30 as a component of a histone deacetylase complex conserved among eukaryotic organisms (Zhang, 1998).

Eukaryotic organisms from yeast to human contain a multiprotein complex that includes Rpd3 histone deacetylase and Sin3 corepressor. The Sin3-Rpd3 complex, when recruited to promoters by specific DNA-binding proteins, can direct transcriptional repression of specific classes of target genes. It has been proposed that the histone deacetylase activity of Rpd3 is important for repression, but direct evidence is lacking. Four Rpd3 derivatives are described with mutations in evolutionarily invariant histidine residues in a putative deacetylation motif. These Rpd3 mutants lack detectable histone deacetylase activity in vitro, but interact normally with Sin3 in vivo. In yeast cells, these catalytically inactive mutants are defective for transcriptional repression. They retain some residual Rpd3 function in vivo, however, suggesting that repression by the Sin3-Rpd3 complex may not be attributable exclusively to its intrinsic histone deacetylase activity. A human Rpd3 homolog can interact with yeast Sin3 and repress transcription when artificially recruited to a promoter. These results suggest that the histone deacetylase activity of Rpd3 is important, but perhaps not absolutely required, for transcriptional repression in vivo (Kadosh, 1998a).

Eukaryotic organisms contain a multiprotein complex that includes Rpd3 histone deacetylase and the Sin3 corepressor. The Sin3-Rpd3 complex is recruited to promoters by specific DNA-binding proteins, whereupon it represses transcription. By directly analyzing the chromatin structure of a repressed promoter in yeast cells, it has been demonstrated that transcriptional repression is associated with localized histone deacetylation. Specifically, decreased acetylation of histones H3 and H4 (preferentially lysines 5 and 12) is observed that depends on the DNA-binding repressor (Ume6), Sin3, and Rpd3. Mapping experiments indicate that the domain of histone deacetylation is highly localized, occurring over a range of one to two nucleosomes. Taken together with previous observations, these results define a novel mechanism of transcriptional repression which involves targeted recruitment of a histone-modifying activity and localized perturbation of chromatin structure (Kadosh, 1998b).

YY1 is a mammalian zinc-finger transcription factor with unusual structural and functional features. It has been implicated as a positive and a negative regulatory factor that binds to the CCATNTT consensus DNA element located in promoters of many cellular and viral genes. A mammalian cDNA that encodes a YY1-binding protein and possesses sequence homology with the yeast transcriptional factor RPD3 has been identified. A Gal4 DNA binding domain-mammalian RPD3 fusion protein strongly represses transcription from a promoter containing Gal4 binding sites. Association between YY1 and mammalian RPD3 requires a glycine-rich region on YY1. Mutations in this region abolish the interaction with mammalian RPD3 and eliminate transcriptional repression by YY1. These data suggest that YY1 negatively regulates transcription by tethering RPD3 to DNA as a cofactor and that this transcriptional mechanism is highly conserved from yeast to human (Yang, 1996).

Three families of prolyl isomerases have been identified: cyclophilins, FK506-binding proteins (FKBPs) and parvulins. All 12 cyclophilins and FKBPs are dispensable for growth in yeast, whereas the one parvulin homolog, Ess1, is essential. Cyclophilin A becomes essential when Ess1 function is compromised. Overexpression of cyclophilin A suppresses ess1 conditional and null mutations, and cyclophilin A enzymatic activity is required for suppression. These results indicate that cyclophilin A and Ess1 function in parallel pathways and act on common targets by a mechanism that requires prolyl isomerization. Using genetic and biochemical approaches, it has been found that one of these targets is the Sin3-Rpd3 histone deacetylase complex, and that cyclophilin A increases and Ess1 decreases disruption of gene silencing by this complex. Conditions that favor acetylation over deacetylation suppress ess1 mutations. These findings support a model in which Ess1 and cyclophilin A modulate the activity of the Sin3-Rpd3 complex, and excess histone deacetylation causes mitotic arrest in ess1 mutants (Arevalo-Rodríguez, 2000).

Two suppressors, Cth1 and Sap30, require cyclophilin A to restore viability in ess1 mutants and may represent common targets of cyclophilin A and Ess1. Sap30 is found in a complex with the Sin3 and Rpd3 proteins, which are components of the yeast HDAC. While Sap30 lacks serine-prolyl or threonine-prolyl sequences that are the known substrates of Ess1, both Sin3 and Rpd3 have multiple Ser-Pro or Thr-Pro sites. Thus, one plausible model is that Ess1 interacts with Sin3 or Rpd3 to catalyze isomerization events required for protein folding and assembly of the HDAC. In accord with this model, biochemical studies reveal that interaction of Ess1 with the Sin3-Rpd3 HDAC is mediated by Sin3. Interaction between cyclophilin A and Sap30 is disrupted by deletion of SIN3, although weak binding to Rpd3 is still detected, indicating that interaction between cyclophilin A and Rpd3 can be Sin3 independent. Most interestingly, the yeast cyclophilin 40 homologs Cpr6 and Cpr7 were identified originally in a two-hybrid screen with the Rpd3 subunit of histone deacetylase and shown to interact directly with Rpd3 in vitro and in vivo in the yeast two-hybrid assay. These findings suggest that cyclophilin A, as well as Cpr6 and Cpr7, functionally and physically interact with Rpd3 (Arevalo-Rodríguez, 2000).

What is the connection between Rpd3 and the cell cycle arrest exhibited by ess1 mutants? In mammalian cells, the histone deacetylase inhibitors TsA and trapoxin induce G1 and G2 phase cell cycle arrest, indicating an involvement of histone deacetylase activity in cell cycle progression. Deletion of RPD3 increases the life span in yeast, suggesting a correlation between aging and rDNA silencing. Loss of silencing at the rDNA array observed in the ess1ts mutant is not likely to be the cause of the mitotic arrest, because deletion of the SIN3 or SAP30 genes, both of which are required for disruption of silencing, does not rescue ess1ts mutants. Moreover, overexpression of Sap30 suppresses ess1ts mutations (Arevalo-Rodríguez, 2000).

What is the mechanism by which Sap30 suppresses ess1ts mutations? One possibility is that overexpression of Sap30 diverts Rpd3 from its cellular targets involved in cell cycle arrest. It has been found that yeast Sap30 can repress transcription in a sin3 mutant, suggesting that Sap30 can interact with and recruit Rpd3 directly to a promoter in a Sin3-independent manner. Taken together, these findings support a model in which overexpression of Sap30 recruits Rpd3 to function in silencing, relieving Rpd3 repression of downstream target genes that are required for mitotic progression (Arevalo-Rodríguez, 2000).

Sap30 requires cyclophilin A for suppression. Overexpression of cyclophilin A decreases silencing at the rDNA loci, indicating that cyclophilin A counteracts this function of Ess1. However, cyclophilin A also suppresses ess1 mutations. It is proposed that both prolyl isomerases catalyze protein conformational changes required for the assembly or activity of the Sin3-Rpd3 complex. Biochemical studies are consistent with a model in which Ess1 directly interacts with the Sin3 component of HDAC, whereas cyclophilin A interacts directly with Rpd3. In this model, Ess1 functions to down-regulate the histone deacetylase activity of Rpd3; the decreased silencing observed in ess1 mutants then results from deregulated, hyperactive Sin3-Rpd3 complexes. Cyclophilin A would catalyze conformational changes in Rpd3 and/or Sap30 that recruit Sap30 to the Rpd3-Sin3 complex and regulate silencing. Overexpression of cyclophilin A (or of Sap30, in a cyclophilin A-dependent fashion) drives the equilibrium toward the formation of a Sin3-Rpd3-Sap30 complex that is still competent to disrupt silencing, but that has a reduced capacity to interact with downstream targets mediating cell cycle arrest. Mitotic arrest in ess1 mutants is the result of misregulation of genes caused by aberrant RNA polymerase II transcription. Further studies will be required to examine in detail the physical interactions of Ess1 and cyclophilin A with the Sin3-Rpd3 HDAC, and to examine how Ess1 and cyclophilin regulate histone deacetylase activity (Arevalo-Rodríguez, 2000).

The yeast Isw2 chromatin remodeling complex functions in parallel with the Sin3-Rpd3 histone deacetylase complex to repress early meiotic genes upon recruitment by Ume6p. For many of these genes, the effect of an isw2 mutation is partially masked by a functional Sin3-Rpd3 complex. To identify the full range of genes repressed or activated by these factors and uncover hidden targets of Isw2-dependent regulation, full genome expression analyses were performed using cDNA microarrays. The Isw2 complex was found to function mainly in repression of transcription in a parallel pathway with the Sin3-Rpd3 complex. In addition to Ume6 target genes, many Ume6-independent genes are derepressed in mutants lacking functional Isw2 and Sin3-Rpd3 complexes. Conversely, ume6 mutants, but not isw2 sin3 or isw2 rpd3 double mutants, have reduced fidelity of mitotic chromosome segregation, suggesting that one or more functions of Ume6p are independent of Sin3-Rpd3 and Isw2 complexes. Chromatin structure analyses of two nonmeiotic genes reveal increased DNase I sensitivity within their regulatory regions in an isw2 mutant. These data suggest that the Isw2 complex functions at Ume6-dependent and -independent loci to create DNase I-inaccessible chromatin structure by regulating the positioning or placement of nucleosomes (Fazzio, 2001).

Histone deacetylases (HDACs) are important for gene regulation and the maintenance of heterochromatin in eukaryotes. Schizosaccharomyces pombe was used as a model system to investigate the functional divergence within this conserved enzyme family. S. pombe has three HDACs encoded by the hda1(+), clr3(+), and clr6(+) genes. Strains mutated in these genes to display strikingly different phenotypes when assayed for viability, chromosome loss, and silencing. Here, conserved differences in the substrate binding pocket identify Clr6 and Hda1 as class I HDACs, while Clr3 belongs in the class II family. Furthermore, these HDACs have strikingly different subcellular localization patterns. Hda1 is localized to the cytoplasm, while most of Clr3 resides throughout the nucleus. Finally, Clr6 is localized exclusively on the chromosomes in a spotted pattern. Interestingly, Clr3, the only HDAC present in the nucleolus, is required for ribosomal DNA (rDNA) silencing. Clr3 presumably acts directly on heterochromatin, since it colocalizes with the centromere, mating-type region, and rDNA as visualized by in situ hybridization. In addition, Clr3 can be cross-linked to mat3 in chromatin immunoprecipitation experiments. Western analysis of bulk histone preparations indicate that Hda1 (class I) had a generally low level of activity in vivo and Clr6 (class I) has a high level of activity and broad in vivo substrate specificity, whereas Clr3 (class II) displays its main activity on acetylated lysine 14 of histone H3. Thus, the distinct functions of the S. pombe HDACs are likely explained by their distinct cellular localization and their different in vivo specificities (Bjerling, 2002).

Saccharomyces cerevisiae has a global pattern of histone acetylation in which histone H3 and H4 acetylation levels are lower at protein-coding sequences than at promoter regions. The loss of Eaf3, a subunit of the NuA4 histone acetylase and Rpd3 histone deacetylase complexes, greatly alters the genomic profile of histone acetylation, with the effects on H4 appearing to be more pronounced than those on H3. Specifically, the loss of Eaf3 causes increases in H3 and H4 acetylation at coding sequences and decreases at promoters, such that histone acetylation levels become evenly distributed across the genome. Eaf3 does not affect the overall level of H4 acetylation, the recruitment of the NuA4 catalytic subunit Esa1 to target promoters, or the level of transcription of the genes analyzed for histone acetylation. Whole-genome transcriptional profiling indicates that Eaf3 plays a positive, but quantitatively modest, role in the transcription of a small subset of genes, whereas it has a negative effect on very few genes. It is suggested that Eaf3 regulates the genomic profile of histone H3 and H4 acetylation in a manner that does not involve targeted recruitment and is independent of transcriptional activity (Reid, 2004).

Mechanism of Rpd3 repression in yeast

Posttranslational modifications of histone tails regulate chromatin structure and transcription. Global analyses are presented of histone acetylation and histone H3 Lys 4 methylation patterns in yeast. A significant correlation is observed between acetylation of histones H3 and H4 in promoter regions and transcriptional activity. In contrast, dimethylation of histone H3 Lys 4 in coding regions correlates with transcriptional activity. The histone methyltransferase Set1 is required to maintain expression of these active, promoter-acetylated, and coding region-methylated genes. Global comparisons reveal that genomic regions deacetylated by the yeast enzymes Rpd3 and Hda1 overlap extensively with Lys 4 hypo- but not hyper-methylated regions. In the context of recent studies showing that Lys 4 methylation precludes histone deacetylase recruitment, it is concluded that Set1 facilitates transcription, in part by protecting active coding regions from deacetylation (Bernstein, 2002).

Certain DNA-binding repressors inhibit transcription by recruiting Rpd3 histone deacetylase complexes to promoters and generating domains of histone deacetylation that extend over a limited number of nucleosomes. The degree of Rpd3-dependent repression depends on the activator and the level of activation, not the extent of histone deacetylation. In all cases tested, activator binding is unaffected by histone deacetylation. In contrast, Rpd3-dependent repression is associated with decreased occupancy by TATA binding protein (TBP), the Swi/Snf nucleosome-remodeling complex, and the SAGA histone acetylase complex. Transcriptional repression is bypassed by direct recruitment of TBP and several TBP-associated factors, but not by natural activation domains or direct recruitment of polymerase II holoenzyme components. These results suggest that the domain of localized histone deacetylation generated by recruitment of Rpd3 mediates repression by inhibiting recruitment of chromatin-modifying activities and TBP (Deckert, 2002).

In the eukaryotic genome, transcriptionally silent chromatin tends to propagate along a chromosome and encroach upon adjacent active chromatin. The silencing machinery can be stopped by chromatin boundary elements. A screen was performed in Saccharomyces cerevisiae for proteins that may contribute to the establishment of a chromatin boundary. It was found that disruption of histone deacetylase Rpd3p results in defective boundary activity, leading to a Sir-dependent local propagation of transcriptional repression. In rpd3δ cells, the amount of Sir2p that was normally found in the nucleolus decreased and the amount of Sir2p found at telomeres and at HM and its adjacent loci increased, leading to an extension of silent chromatin in those areas. In addition, Rpd3p interacts directly with chromatin at boundary regions to deacetylate histone H4 at lysine 5 and at lysine 12. Either the mutation of histone H4 at lysine 5 or a decrease in the histone acetyltransferase (HAT) activity of Esa1p abrogated the silencing phenotype associated with rpd3 mutation, suggesting a novel role for the H4 amino terminus in Rpd3p-mediated heterochromatin boundary regulation. Together, these data provide insight into the molecular mechanisms for the anti-silencing functions of Rpd3p during the formation of heterochromatin boundaries (Zhou, 2009).

Yeast histone deacetylases target specific genes

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