Nps1/Sth1p, a component of an essential chromatin-remodeling complex of Saccharomyces cerevisiae, is required for the maximal expression of early meiotic genes

COMPASS and SWI/SNF complexes in development and disease

The Trithorax group (TrxG) of proteins is a large family of epigenetic regulators that form multiprotein complexes to counteract repressive developmental gene expression programmes established by the Polycomb group of proteins and to promote and maintain an active state of gene expression. Recent studies are providing new insights into how two crucial families of the TrxG - the COMPASS family of histone H3 lysine 4 methyltransferases and the SWI/SNF family of chromatin remodelling complexes - regulate gene expression and developmental programmes, and how misregulation of their activities through genetic abnormalities leads to pathologies such as developmental disorders and malignancies.

RSC Chromatin-Remodeling Complex Is Important for Mitochondrial Function in Saccharomyces cerevisiae

RSC (Remodel the Structure of Chromatin) is an ATP-dependent chromatin remodeling complex essential for the growth of Saccharomyces cerevisiae. RSC exists as two distinct isoforms that share core subunits including the ATPase subunit Nps1/Sth1 but contain either Rsc1or Rsc2. Using the synthetic genetic array (SGA) of the non-essential null mutation method, we screened for mutations exhibiting synthetic growth defects in combination with the temperature-sensitive mutant, nps1-105, and found connections between mitochondrial function and RSC. rsc mutants, including rsc1Δ, rsc2Δ, and nps1-13, another temperature-sensitive nps1 mutant, exhibited defective respiratory growth; in addition, rsc2Δ and nps1-13 contained aggregated mitochondria. The rsc2Δ phenotypes were relieved by RSC1 overexpression, indicating that the isoforms play a redundant role in respiratory growth. Genome-wide expression analysis in nps1-13 under respiratory conditions suggested that RSC regulates the transcription of some target genes of the HAP complex, a transcriptional activator of respiratory gene expression. Nps1 physically interacted with Hap4, the transcriptional activator moiety of the HAP complex, and overexpression of HAP4 alleviated respiratory defects in nps1-13, suggesting that RSC plays pivotal roles in mitochondrial gene expression and shares a set of target genes with the HAP complex.

Interplay between modifications of chromatin and meiotic recombination hotspots

Meiotic recombination lies at the heart of sexual reproduction. It is essential for producing viable gametes with a normal haploid genomic content and its dysfunctions can be at the source of aneuploidies, such as the Down syndrome, or many genetic disorders. Meiotic recombination also generates genetic diversity that is transmitted to progeny by shuffling maternal and paternal alleles along chromosomes. Recombination takes place at non-random chromosomal sites called 'hotspots'. Recent evidence has shown that their location is influenced by properties of chromatin. In addition, many studies in somatic cells have highlighted the need for changes in chromatin dynamics to allow the process of recombination. In this review, we discuss how changes in the chromatin landscape may influence the recombination map, and reciprocally, how recombination events may lead to epigenetic modifications at sites of recombination, which could be transmitted to progeny.

The Rpd3/HDAC complex is present at the URS1 cis-element with hyperacetylated histone H3

In eukaryotes, the hypoacetylated state of histone N-terminal lysines at many gene-promoters, which is created by histone deacetylases (HDACs), is changed to the hyperacetylated state by the function of histone acetyltransferases (HATs) upon transcription activation. Although much insight has been obtained to date as to how modification of the histone tail regulates gene expression, little is known about how the transition between the unmodified and modified states takes place. In Saccharomyces cerevisiae, the HDAC complex containing Rpd3 (Rpd3L) represses the transcription of several sets of genes through the URS1 cis-element. We found that the histone H3 acetylation level at the URS1 of seven genes (INO1, CAT2, ACS1, YAT1, RIM4, CRC1, and SIP4) was elevated in the presence of Rpd3/HDAC in growth in acetate-containing medium (YPA), suggesting that a mechanism that regulates HDAC activity is present in this organism. The biological significance of this phenomenon is discussed below.

Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation

An important issue for chromatin remodeling complexes is how their bromodomains recognize particular acetylated lysine residues in histones. The Rsc4 subunit of the yeast remodeler RSC contains an essential tandem bromodomain (TBD) that binds acetylated K14 of histone H3 (H3K14ac). We report a series of crystal structures that reveal a compact TBD that binds H3K14ac in the second bromodomain and, remarkably, binds acetylated K25 of Rsc4 itself in the first bromodomain. Endogenous Rsc4 is acetylated only at K25, and Gcn5 is identified as necessary and sufficient for Rsc4 K25 acetylation in vivo and in vitro. Rsc4 K25 acetylation inhibits binding to H3K14ac, and mutation of Rsc4 K25 results in altered growth rates. These data suggest an autoregulatory mechanism in which Gcn5 performs both the activating (H3K14ac) and inhibitory (Rsc4 K25ac) modifications, perhaps to provide temporal regulation. Additional regulatory mechanisms are indicated as H3S10 phosphorylation inhibits Rsc4 binding to H3K14ac peptides.

Interplay between chromatin and trans-acting factors on the IME2 promoter upon induction of the gene at the onset of meiosis

The IME2 gene is one of the key regulators of the initiation of meiosis in budding yeast. This gene is repressed during mitosis through the repressive chromatin structure at the promoter, which is maintained by the Rpd3-Sin3 histone deacetylase (HDAC) complex. IME2 expression in meiosis requires Gcn5/histone acetyltransferase, the transcriptional activator Ime1, and the chromatin remodeler RSC; however, the molecular basis of IME2 activation had not been previously defined. We found that, during mitotic growth, a nucleosome masked the TATA element of IME2, and this positioning depended on HDAC. This chromatin structure was remodeled at meiosis by RSC that was recruited to TATA by Ime1. Stable tethering of Ime1 to the promoter required the presence of Gcn5. Interestingly, Ime1 binding to the promoter was kept at low levels during the very early stages in meiosis, even when the levels of Ime1 and histone H3 acetylation at the promoter were at their highest, making a 4- to 6-h delay of the IME2 expression from that of IME1. HDAC was continuously present at the promoter regardless of the transcriptional condition of IME2, and deletion of RPD3 allowed the IME2 expression shortly after the expression of IME1, suggesting that HDAC plays a role in regulating the timing of IME2 expression.

RSC1 and RSC2 are required for expression of mid-late sporulation-specific genes in Saccharomyces cerevisiae

Rsc1 and Rsc2 are alternative bromodomain-containing subunits of the ATP-dependent RSC chromatin remodeling complex in Saccharomyces cerevisiae. Smk1 is a sporulation-specific mitogen-activated protein kinase homolog that is required for the postmeiotic events of spore formation. In this study we show that RSC1 and RSC2 are haploinsufficient for spore formation in a smk1 hypomorph. Moreover, diploids lacking Rsc1 or Rsc2 show a subset of smk1-like phenotypes. High-copy-number RSC1 plasmids do not suppress rsc2-Delta/rsc2-Delta sporulation defects, and high-copy-number RSC2 plasmids do not suppress rsc1-Delta/rsc1-Delta sporulation defects. Mid-late sporulation-specific genes, which are normally expressed while key steps in spore assembly occur and which include genes that are required for spore wall formation, are not expressed in cells lacking Rsc1 or Rsc2. We speculate that the combined action of Rsc1 and Rsc2 at mid-late promoters is specifically required for the proper expression of this uniquely timed set of genes. Our data suggest that Smk1 and Rsc1/2 define parallel pathways that converge to provide signaling information and the expression of gene products, respectively, that are required for spore morphogenesis.

Genetic analysis of RSC58, which encodes a component of a yeast chromatin remodeling complex, and interacts with the transcription factor Swi6

Before transcription can begin, the chromatin structure must be rearranged at the nucleosome level. In yeast the nucleosome remodeling complex RSC is involved in this process and it is essential for growth. Recent analysis of the RSC by mass spectrometry has suggested that the product of YLR033w, an essential gene of unknown function, is a novel component of the complex, and the gene has been renamed RSC58. Rsc58 is predicted to be 502 amino acids long. We have isolated five temperature-sensitive mutations in RSC58 and studied the cellular function of the gene. Our major findings are the following. (1) Two of the alleles have a frameshift mutation near the 3' end of the gene, in codons 482 and 485, respectively. The first mutation is associated with the more severe phenotype. This is compatible with the finding that removal of the C-terminal 25 residues of Rsc58 is lethal to cells. These results suggest that C-terminal region is essential for Rsc58 function. (2) RSC4, which codes for another member of the RSC, was found to be a multicopy suppressor of the phenotype of one of the temperature-sensitive mutants. (3) Two-hybrid analysis identified Swi6, a transcription factor, as a candidate interactor with Rsc58. An interaction between Rsc58 and Swi6 is also suggested by the fact that rsc58-ts Deltaswi6 double mutants show a more severe growth defect than either mutation alone. These results suggest the possibility that Rsc58 mediates between nucleosome remodeling and the initiation of transcription.

The RSC nucleosome-remodeling complex is required for Cohesin's association with chromosome arms

The fidelity of chromosome segregation requires that the cohesin protein complex bind together newly replicated sister chromatids both at centromeres and at discrete sites along chromosome arms. Segregation of the yeast 2 micro plasmid also requires cohesin, which is recruited to the plasmid partitioning locus. Here we report that the RSC chromatin-remodeling complex regulates the differential association of cohesin with centromeres and chromosome arms. RSC cycles on and off chromosomal arm and plasmid cohesin binding sites in a cell cycle-regulated manner 15 min preceding Mcd1p, the central cohesin subunit. We show that in rsc mutants Mcd1p fails to associate with chromosome arms but still binds to centromeres, and that consequently, the arm regions of mitotic sister chromosomes separate precociously while cohesion at centromeres is unaffected. Our data suggest a role for RSC in facilitating the loading of cohesin specifically onto chromosome arms, thereby ensuring sister chromatid cohesion and proper chromosome segregation.

Signal pathway integration in the switch from the mitotic cell cycle to meiosis in yeast

Diploid yeast, like most eukaryotes, can undergo meiotic differentiation to form haploid gametes. Meiotic differentiation and cell growth (proliferation) are mutually exclusive programs, and in yeast the switch between growth and meiosis is controlled by nutritional signals. The signaling pathways that mediate nutritional controls on meiotic initiation fall into three broad classes: those that respond to nutrient starvation, those that respond to non-fermentable carbon sources, and those that respond to glucose. At the onset of meiosis, nutritional signaling pathways converge on transcriptional regulation of two genes: IME1, which encodes a transcription factor; and IME2, which encodes a protein kinase. Transcription of IME1 and IME2 trigger initiation of meiosis, and the expression of these two genes is linked with one other, with expression of later meiotic genes and with early meiotic events such as DNA replication. In addition, the signaling pathways that control IME1 and IME2 expression are themselves integrated through a variety of mechanisms. Thus the signal network that controls the switch from growth to meiotic differentiation provides a signaling code that translates different combinations of extracellular signals into appropriate cellular responses.

The SWI/SNF family of ATP-dependent chromatin remodelers: similar mechanisms for diverse functions

The SWI/SNF family of complexes utilizes the energy of ATP hydrolysis to remodel chromatin structures, thereby allowing transcription factors to gain access to DNA. Recent studies suggest that these remodelers also participate in other DNA metabolic reactions such as replication and viral integration, and even in control of cell growth and tumor suppression. The SWI/SNF remodelers can be classified into at least two distinct subfamilies: one includes human BAF (also known as hSWI/SNF-A) and yeast SWI/SNF; the other comprises human PBAF (hSWI/SNF-B) and yeast RSC. Although both types of complexes have similar subunit composition and chromatin remodeling activity in vitro, they cannot replace each other during transcription mediated by specific activators. Thus, each remodeler probably works with a specific set of activators during gene activation. The availability of distinct types of remodelers can allow cells to regulate expression of a specific group of genes by modulating the activity of corresponding remodelers.

Regulation of the premiddle and middle phases of expression of the NDT80 gene during sporulation of Saccharomyces cerevisiae

The NDT80 gene of Saccharomyces cerevisiae, which encodes a global activator of transcription of middle sporulation-specific genes, is first expressed after the activation of early meiotic genes but prior to activation of middle sporulation-specific genes. Both upstream repression sequence 1 (URS1) and mid-sporulation element (MSE) sites are present in the promoter region of the NDT80 gene; these elements have been shown previously to contribute to the regulation of expression of early and middle sporulation-specific genes, respectively, by mediating repression in growing cells and activation at specific times during sporulation. In this study, we have shown that the overlapping windows of URS1- and MSE-mediated repression and activation are responsible for the distinctive premiddle expression pattern of the NDT80 gene. Our data suggest that a Sum1-associated repression complex bound at the NDT80 MSE sites prevents Ime1 tethered at the NDT80 URS1 sites from activating transcription of the NDT80 gene at the time that Ime1-dependent activation of early URS1-regulated meiotic genes is occurring. We propose that a decrease in the efficiency of Sum1-mediated repression as cells progress through the early events of the sporulation program allows the previously inactive Ime1 tethered at the URS1(NDT80) sites to promote a low level of expression of the NDT80 gene. This initial phase of URS1-dependent NDT80 expression is followed by Ndt80-dependent upregulation of its own expression, which requires the MSE(NDT80) sites and occurs concomitantly with Ndt80-dependent activation of a set of middle MSE-regulated sporulation-specific genes. Mutation of IME2 prevents expression of NDT80 in sporulating cells. We show in this study that NDT80 is expressed and that middle genes are activated in cells of an Deltaime2/Deltaime2 Deltasum1/Deltasum1 strain in sporulation medium. This suggests that Ime2 activates expression of NDT80 by eliminating Sum1-mediated repression.

RSC2, encoding a component of the RSC nucleosome remodeling complex, is essential for 2 microm plasmid maintenance in Saccharomyces cerevisiae

The stable maintenance of the 2 microm circle plasmid depends on its ability to overcome intrinsic maternal inheritance bias, which in yeast normally results in the failure to transmit DNA molecules efficiently to daughter cells. In addition to the plasmid proteins Rep1 and Rep2 acting on the plasmid DNA locus STB, it is likely that other chromosomally encoded yeast proteins are required. We have isolated mutants of yeast unable to maintain 2 microm and found that RSC2 is essential for 2 microm to overcome maternal inheritance bias. Rsc2 is part of a multisubunit RSC chromatin remodeling complex, and we show that in the absence of Rsc2 the chromatin structure of the STB region is significantly altered and the Rep1 protein loses its normal localization to subnuclear foci. Rsc1, a closely related homolog of Rsc2 present in an alternative form of the RSC complex, is not required for 2 microm maintenance and does not replace the requirement for Rsc2 when overexpressed. This represents the first specific role for Rsc2 that has been related to a change in chromatin structure, as well as the first direct evidence linking chromatin structure to 2 microm segregation.

Yeast RSC function is required for organization of the cellular cytoskeleton via an alternative PKC1 pathway

RSC is a 15-protein ATP-dependent chromatin-remodeling complex related to Snf-Swi, the prototypical ATP-dependent nucleosome remodeler in budding yeast. Despite insight into the mechanism by which purified RSC remodels nucleosomes, little is known about the chromosomal targets or cellular pathways in which RSC acts. To better understand the cellular function of RSC, a screen was undertaken for gene dosage suppressors of sth1-3ts, a temperature-sensitive mutation in STH1, which encodes the essential ATPase subunit. Slg1p and Mid2p, two type I transmembrane stress sensors of cell wall integrity that function upstream of protein kinase C (Pkc1p), were identified as multicopy suppressors of sth1-3ts cells. Although the sth1-3ts mutant exhibits defects characteristic of PKC1 pathway mutants (caffeine and staurosporine sensitivities and an osmoremedial phenotype), only upstream components and not downstream effectors of the PKC1-MAP kinase pathway can suppress defects conferred by sth1-3ts, suggesting that RSC functions in an alternative PKC1-dependent pathway. Moreover, sth1-3ts cells display defects in actin cytoskeletal rearrangements and are hypersensitive to the microtubule depolymerizing drug, TBZ; both of these defects can be corrected by the high-copy suppressors. Together, these data reveal an important functional connection between the RSC remodeler and PKC1-dependent signaling in regulating the cellular architecture.

Functional differences between RSC1 and RSC2, components of a for growth essential chromatin-remodeling complex of Saccharomyces cerevisiae, during the sporulation process

RSC, a for growth essential chromatin-remodeling complex of Saccharomyces cerevisiae, is composed of 15 subunits. Rsc1p and Rsc2p are highly homologous proteins and are contained in distinct RSC complexes. We found that both rsc1Delta and rsc2Delta homozygous diploids showed reduced sporulation with decreased expression of IME2 and that rsc1Delta, but not rsc2Delta, produced aberrant asci containing one to three spores. Overexpression of RSC2 in rsc1Delta recovered the sporulation efficiency but not the production of aberrant asci. In contrast, overexpression of RSC1 in rsc2Delta did not alleviate its sporulation defect. These results suggest that both Rsc1p and Rsc2p share overlapping functions on IME2 expression, with a prominent role for Rsc2p, whereas Rsc1p has an additional function in the late steps of the sporulation process.

The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress

The cellular response to environmental changes includes widespread modifications in gene expression. Here we report the identification and characterization of Rsc9, a member of the RSC chromatin-remodeling complex in yeast. The genome-wide localization of Rsc9 indicated a relationship between genes targeted by Rsc9 and genes regulated by stress; treatment with hydrogen peroxide or rapamycin, which inhibits TOR signaling, resulted in genome-wide changes in Rsc9 occupancy. We further show that Rsc9 is involved in both repression and activation of mRNAs regulated by TOR as well as the synthesis of rRNA. Our results illustrate the response of a chromatin-remodeling factor to signaling cascades and suggest that changes in the activity of chromatin-remodeling factors are reflected in changes in their localization in the genome.

PKC1, a protein kinase C homologue of Saccharomyces cerevisiae, participates in microtubule function through the yeast EB1 homologue, BIM1

BACKGROUND

RSC is a chromatin-remodelling complex of Saccharomyces cerevisiae and essential for growth. Its catalytic subunit is encoded by the NPS1/STH1 gene. At the present time, little is known regarding the cellular function of RSC.

RESULTS

To identify genes with functions related to NPS1, we screened high-copy suppressor genes for the temperature- and thiabendazole (TBZ)-sensitive mutant allele of NPS1, nps1-105. Amongst the suppressors we cloned PKC1/STT1 and BIM1 that encoded a homologue of mammalian protein kinase C and a conserved microtubule binding protein homologous to human EB1, respectively. Both the temperature sensitive mutation of PKC1, stt1, and the bim1 null mutation caused synthetic growth defects with nps1-105. A genetic analysis of the functional relationships between these genes revealed that PKC1 suppressed the defect of nps1-105 through the BIM1 function but not by the activation of the MPK1/MAPK pathway. The stt1 mutation alone showed TBZ sensitivity and delayed the G2-phase progression at semi-permissive temperatures. Both of these stt1 phenotypes were suppressed by the over-expression of BIM1. In addition, stt1 as well as nps1-105, mis-segregated a mini-chromosome at frequencies higher than the wild-type at a permissive temperature. The mis-segregation was enhanced in the nps1-105 stt1 double mutant.

CONCLUSION

These results suggest that Pkc1p plays a role which is relevant to microtubule functions and that this role is mediated by a hitherto unknown PKC signalling pathway and by Bim1p

The BAH domain, polybromo and the RSC chromatin remodelling complex

The BAH (Bromo-adjacent homology) domain is a domain first identified in the vertebrate polybromo protein, a protein present in a large nuclear complex. Polybromo has two BAH domains, six bromodomains and an HMG-box. The BAH domain has been identified in a number of proteins involved in gene transcription and repression and is likely to be involved in protein-protein interactions. Polybromo resembles two related proteins in yeast, the Rsc1 and Rsc2 proteins, both having a BAH domain and two bromodomains as well as a DNA binding motif, the AT -hook. The Rsc1 and 2 proteins are components of the RSC (remodelling the structure of chromatin) complex and are required for transcriptional control. In this paper we review recent data on the function of the BAH and bromodomains in relation to polybromo and the Rsc proteins.

When the SWI/SNF complex remodels...the cell cycle

Mammalian cells contain several chromatin-remodeling complexes associated with the Brm and Brg1 helicase-like proteins. These complexes likely represent the functional homologs of the SWI/SNF and RSC complexes found in Saccharomyces cerevisiae. The mammalian chromatin-remodeling complexes are involved in both activation and repression of a variety of genes. Several lines of evidence also indicate that they play a specific role in the regulation of cell growth. Brm is down-regulated by ras signaling and its forced re-expression suppresses transformation by this oncogene. Besides, the Brg1 gene is silenced or mutated in several tumors cell lines and a Brg1-associated complex was recently found to co-purify with BRCA1, involved in breast and ovarian cancers. Finally, the gene encoding SNF5/Ini1, a subunit common to all mammalian SWI/SNF complexes, is inactivated in rhabdoid sarcomas, a very aggressive form of pediatric cancer. The current review will address observations made upon inactivation of Brm, Brg1 and SNF5/Ini1 by homologous recombination in the mouse, as well as the possible implication of these factors in the regulation of the Retinoblastoma pRb-mediated repression of the transcription factor E2F.

The human SWI/SNF-B chromatin-remodeling complex is related to yeast rsc and localizes at kinetochores of mitotic chromosomes

The SWI/SNF family of chromatin-remodeling complexes facilitates gene expression by helping transcription factors gain access to their targets in chromatin. SWI/SNF and Rsc are distinctive members of this family from yeast. They have similar protein components and catalytic activities but differ in biological function. Rsc is required for cell cycle progression through mitosis, whereas SWI/SNF is not. Human complexes of this family have also been identified, which have often been considered related to yeast SWI/SNF. However, all human subunits identified to date are equally similar to components of both SWI/SNF and Rsc, leaving open the possibility that some or all of the human complexes are rather related to Rsc. Here, we present evidence that the previously identified human SWI/SNF-B complex is indeed of the Rsc type. It contains six components conserved in both Rsc and SWI/SNF. Importantly, it has a unique subunit, BAF180, that harbors a distinctive set of structural motifs characteristic of three components of Rsc. Of the two mammalian ATPases known to be related to those in the yeast complexes, human SWI/SNF-B contains only the homolog that functions like Rsc during cell growth. Immunofluorescence studies with a BAF180 antibody revealed that SWI/SNF-B localizes at the kinetochores of chromosomes during mitosis. Our data suggest that SWI/SNF-B and Rsc represent a novel subfamily of chromatin-remodeling complexes conserved from yeast to human, and could participate in cell division at kinetochores of mitotic chromosomes.

Saccharomyces cerevisiae gene ISW2 encodes a microtubule-interacting protein required for premeiotic DNA replication

A molecular genetic characterization of the ORF YOR304W (ISW2), identified in a screen of a yeast lambdagt11 library using a monoclonal antibody that reacts with a 210 kDa mammalian microtubule-interacting protein, is presented in this paper. The protein encoded by the ORF YOR304W is 50% identical to the Drosophila nucleosome remodelling factor ISWI and is therefore a new member of the SNF2 protein family and has been recently entered into SDG as ISW2. Although not essential for vegetative growth, we found that the ISW2 gene is required for early stages in sporulation. The isw2 homozygous deletant diploid strain was blocked in the G(1) phase of the cell cycle, unable to execute the premeiotic DNA replication and progress through the nuclear meiotic division cycle. ISW2 expression from a multicopy plasmid had the same effect as deletion, but ISW2 expression from a centromeric plasmid rescued the deletion phenotype. In vegetatively growing diploid cells, the Isw2 protein was preferentially found in the cytoplasm, co-localizing with microtubules. An accumulation of the Isw2 protein within the nucleus was observed in cells entering sporulation. Together with data published very recently by Tsukiyama et al. (1999), we propose a role for the Isw2 protein in facilitating chromatin accessibility for transcriptional factor(s) that positively regulate meiosis/sporulation-specific genes.

Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains

RSC is an essential 15 protein nucleosome-remodeling complex from S. cerevisiae. We have identified two closely related RSC members, Rsc1 and Rsc2. Biochemical analysis revealed Rsc1 and Rsc2 in distinct complexes, defining two forms of RSC. Genetic analysis has shown that Rsc1 and Rsc2 possess shared and unique functions. Rsc1 and Rsc2 each contain two bromodomains, a bromo-adjacent homology (BAH) domain, and an AT hook. One of the bromodomains, the BAH domain, and the AT hook are each essential for Rsc1 and Rsc2 functions, although they are not required for assembly into RSC complexes. Therefore, these domains are required for RSC function. Additional genetic analysis provides further evidence that RSC function is related to transcriptional control.