A position effect in the control of transcription at yeast mating type loci

Multifaceted functions of RNA-binding protein vigilin in gene silencing, genome stability, and autism-related disorders

RNA-binding proteins (RBPs) are emerging as important players in regulating eukaryotic gene expression and genome stability. Specific RBPs have been shown to mediate various chromatin-associated processes ranging from transcription to gene silencing and DNA repair. One of the prominent classes of RBPs is the KH domain-containing proteins. Vigilin, an evolutionarily conserved KH domain-containing RBP has been shown to be associated with diverse biological processes like RNA transport and metabolism, sterol metabolism, chromosome segregation, and carcinogenesis. We have previously reported that vigilin is essential for heterochromatin-mediated gene silencing in fission yeast. More recently, we have identified that vigilin in humans plays a critical role in efficient repair of DNA double-stranded breaks and functions in homology-directed DNA repair. In this review, we highlight the multifaceted functions of vigilin and discuss the findings in the context of gene expression, genome organization, cancer, and autism-related disorders.

Limits to transcriptional silencing in Saccharomyces cerevisiae

Mating-type switching in the budding yeast Saccharomyces cerevisiae relies on the Sir protein complex to silence HML and HMR, the two loci containing copies of the alleles of the mating type locus, MAT. Sir-based transcriptional silencing has been considered locus-specific, but the recent discovery of rare and transient escapes from silencing at HMLα2 with a sensitive assay called to question if these events extend to the whole locus. Adapting the same assay, we measured that transient silencing failures at HML were more frequent for the α2 gene than α1, similarly to their expression level in unsilenced cells. By coupling a mating assay, at HML we found that one of the two genes at that locus can be transiently expressed while the other gene is maintained silent. Thus, transient silencing loss can be a property of the gene rather than the locus. Cells lacking the SIR1 gene experience epigenetic bistability at HML and HMR. Our previous result led us to ask if HML could allow for two independent epigenetic states within the locus in a sir1Δ mutant. A simple construct using a double fluorescent reporter at HMLα1 and HMLα2 ruled out this possibility. Each HML locus displayed a single epigenetic state. We revisited the question of the correlation between the states of two HML loci in diploid cells, and showed they were independent. Finally, we determined the relative strength of gene repression achieved by Sir-based silencing with that achieved by the a1-α2 repressor.

Sirtuins of parasitic protozoa: in search of function(s)

The SIR2 family of NAD⁺-dependent protein deacetylases, collectively called sirtuins, has been of central interest due to their proposed roles in life-span regulation and ageing. Sirtuins are one group of environment sensors of a cell interpreting external information and orchestrating internal responses at the sub-cellular level, through participation in gene regulation mechanisms. Remarkably conserved across all kingdoms of life SIR2 proteins in several protozoan parasites appear to have both conserved and intriguing unique functions. This review summarises our current knowledge of the members of the sirtuin families in Apicomplexa, including Plasmodium, and other protozoan parasites such as Trypanosoma and Leishmania. The wide diversity of processes regulated by SIR2 proteins makes them targets worthy of exploitation in anti-parasitic therapies.

Regulatory consequences of gene translocation in bacteria

Gene translocations play an important role in the plasticity and evolution of bacterial genomes. In this study, we investigated the impact on gene regulation of three genome organizational features that can be altered by translocations: (i) chromosome position; (ii) gene orientation; and (iii) the distance between a target gene and its transcription factor gene (‘target-TF distance’). Specifically, we quantified the effect of these features on constitutive expression, transcription factor binding and/or gene expression noise using a synthetic network in Escherichia coli composed of a transcription factor (LacI repressor) and its target gene (yfp). Here we show that gene regulation is generally robust to changes in chromosome position, gene orientation and target-TF distance. The only demonstrable effect was that chromosome position alters constitutive expression, due to changes in gene copy number and local sequence effects, and that this determines maximum and minimum expression levels. The results were incorporated into a mathematical model which was used to quantitatively predict the responses of a simple gene network to gene translocations; the predictions were confirmed experimentally. In summary, gene translocation can modulate constitutive gene expression levels due to changes in chromosome position but it has minimal impact on other facets of gene regulation.

A cis-acting tRNA gene imposes the cell cycle progression requirement for establishing silencing at the HMR locus in yeast

Numerous studies have determined that the establishment of Sir protein-dependent transcriptional silencing in yeast requires progression through the cell cycle. In our study we examined the cell cycle requirement for the establishment of silencing at the HML and HMR loci using strains bearing conditional or inducible SIR3 alleles. Consistent with prior reports, we observed that establishing silencing at HMR required progression through the cell cycle. Unexpectedly, we found that the HML locus is far less dependent on cell cycle progression to establish silencing. Seeking cis-acting elements that could account for this difference, we found that deletion of a tRNA gene that serves as a chromatin boundary at HMR abolishes the cell cycle progression requirement at this locus, while insertion of sequences containing this tRNA gene adjacent to HML imposes dependence on cell cycle progression for the full establishment of silencing. Our results indicate that the cell cycle progression requirement is not a property intrinsic to the formation of heterochromatin in yeast, but is instead a cis-limited, locus-specific phenomenon. We show that inactivation of the Scc1 cohesin also abolishes the requirement for cell cycle progression and test models based on a possible link between the tRNA gene and cohesin association.

Negative control for the initiation of meiosis in Schizosaccharomyces pombe

Temperature-sensitive mutants of the pat1 gene of Schizosaccharomyces pombe are able to produce poorly viable spores from the haploid state without the requirement for nitrogen starvation if exposed to the restrictive temperature. Three lines of evidence strongly suggest that this gene codes for a factor whose physiological role is inhibition of initiation of meiosis. First, pat1 haploids arrested in G(1) phase undergo apparent premeiotic DNA synthesis at the restrictive temperature. Second, the pat1 gene was found to exert its function at a specified stage of the meiotic pathway by comparison with other meiotic mutants. Third, meiotic recombination and chromosome segregation take place quite normally in pat1 diploids at the restrictive temperature, resulting in the production of highly viable spores. A negative control mechanism for meiosis is proposed.

The telotype defines the telomere state in Saccharomyces cerevisiae and is inherited as a dominant non-Mendelian characteristic in cells lacking telomerase

Telomeres are an unusual component of the genome because they do not encode genes, but their structure and cellular maintenance machinery (which we define as "telotype") are essential for chromosome stability. Cells can switch between different phenotypic states. One such example is when they switch from maintenance mediated by telomerase (TERT telotype) to one of the two alternative mechanisms of telomere preservation (ALT I and ALT II telotype). The nature of this switch is largely unknown. Reintroduction of telomerase into ALT II, but not ALT I, yeast led to the loss of their ability to survive a second round of telomerase withdrawal. Mating-based genetic analysis of ALT I and II revealed that both types of telomerase-independent telomere maintenance are inherited as a non-Mendelian trait dominant over senescence (SEN telotype). Additionally, inheritance of ALT I and ALT II did not depend on either the mitochondrial genome or a prion-based mechanism. Type I, but not type II, survivor cells exhibited impaired gene silencing, potentially connecting the switch to the ALT telotype epigenetic changes. These data provide evidence that nonprion epigenetic-like mechanisms confer flexibility on cells as a population to adjust to the life-threatening situation of telomerase loss, allowing cells to switch from TERT to ALT telotypes that can sustain viable populations.

Asymmetric positioning of nucleosomes and directional establishment of transcriptionally silent chromatin by Saccharomyces cerevisiae silencers

In Saccharomyces cerevisiae, silencers flanking the HML and HMR loci consist of various combinations of binding sites for Abf1p, Rap1p, and the origin recognition complex (ORC) that serve to recruit the Sir silencing complex, thereby initiating the establishment of transcriptionally silent chromatin. There have been seemingly conflicting reports concerning whether silencers function in an orientation-dependent or -independent manner, and what determines the directionality of a silencer has not been explored. We demonstrate that chromatin plays a key role in determining the potency and directionality of silencers. We show that nucleosomes are asymmetrically distributed around the HML-I or HMR-E silencer so that a nucleosome is positioned close to the Abf1p side but not the ORC side of the silencer. This coincides with preferential association of Sir proteins and transcriptional silencing on the Abf1p side of the silencer. Elimination of the asymmetry in nucleosome positioning at a silencer leads to comparable silencing on both sides. Asymmetric nucleosome positioning in the immediate vicinity of a silencer is independent of its orientation and genomic context, indicating that it is the inherent property of the silencer. Moreover, it is also independent of the Sir complex and thus precedes the formation of silent chromatin. Finally, we demonstrate that asymmetric positioning of nucleosomes and directional silencing by a silencer depend on ORC and Abf1p. We conclude that the HML-I and HMR-E silencers promote asymmetric positioning of nucleosomes, leading to unequal potentials of transcriptional silencing on their sides and, hence, directional silencing.

New alleles of SIR2 define cell-cycle-specific silencing functions

The establishment of transcriptional silencing in yeast requires cell-cycle progression, but the nature of this requirement is unknown. Sir2 is a protein deacetylase that is required for gene silencing in yeast. We have used temperature-sensitive alleles of the SIR2 gene to assess Sir2's contribution to silencing as a function of the cell cycle. When examined in vivo, these conditional alleles fall into two classes: one class exhibits a loss of silencing when raised to the nonpermissive temperature regardless of cell-cycle position, while the second class exhibits a mitosis-specific silencing defect. Alleles of the first class have a primary defect in protein deacetylase activity, while the alleles of the second class are specifically defective in Sir2-Sir4 interactions at nonpermissive temperatures. Using a SIR2 temperature-sensitive allele, we show that silencing can be established at the HML locus during progression through the G2/M-G1 interval. These results suggest that yeast heterochromatin undergoes structural transitions as a function of the cell cycle and support the existence of a critical assembly step for silent chromatin in mitosis.

Mechanism of Transcriptional Silencing in Yeast

Transcriptional silencing is a phenomenon in which the transcription of a gene by RNA polymerase II or III is repressed or not, dependent only on the gene's chromosomal location. Two prevailing models exist for silencing: (1) steric hindrance in silenced chromatin inhibits the binding of upstream activator proteins or polymerase or (2) silencing primarily blocks steps downstream of transcription preinitiation complex formation. Here, we test these models quantitatively for the case of SIR2-dependent silencing in budding yeast, using foreign and endogenous reporter proteins, at transgenic and endogenous loci. Our results contradict both models and show instead that transcriptional silencing at several URA3 transgenes, and at the naturally silenced endogenous HMRa and HMLalpha mating type genes, acts downstream of gene activator protein binding to strongly reduce the occupancy of TFIIB, RNA polymerase II, and TFIIE at the silenced promoters.

DLP, a novel Dim1 family protein implicated in pre-mRNA splicing and cell cycle progression

In eukaryotes, primary transcripts undergo a splicing process that removes intronic sequences by a macromolecular enzyme known as the spliceosome. Both genetic and biochemical studies have revealed that essential components of the spliceosome include five small RNAs, U1, U2, U4, U5, and U6, and as many as 300 distinct proteins. Here we report the molecular cloning and functional analysis of a novel cDNA encoding for a protein of 149 amino acids. This protein has 38% amino acid sequence identity with and is evolutionally related to yeast Dim1 protein. Hence we named this protein DLP for Dim1-like protein. We showed that DLP is required for S/G(2) transition. We also demonstrated that DLP functions in cell nucleus and interacts with the U5-102-kDa protein subunit of the spliceosome, and blocking DLP protein activity led to an insufficient pre-mRNA splicing, suggesting that DLP is yet another protein component involved in pre-mRNA splicing. Collectively, our experiments indicated that DLP is implicated in not only cell cycle progression but also in a more specific molecular process such as pre-mRNA splicing.

Sirtuins: Sir2-related NAD-dependent protein deacetylases

Silent information regulator 2 (Sir2) proteins, or sirtuins, are protein deacetylases dependent on nicotine adenine dinucleotide (NAD) and regulate transcriptional repression, recombination, the cell-division cycle, microtubule organization, and cellular responses to DNA-damaging agents.

Silent information regulator 2 (Sir2) proteins, or sirtuins, are protein deacetylases dependent on nicotine adenine dinucleotide (NAD) and are found in organisms ranging from bacteria to humans. In eukaryotes, sirtuins regulate transcriptional repression, recombination, the cell-division cycle, microtubule organization, and cellular responses to DNA-damaging agents. Sirtuins have also been implicated in regulating the molecular mechanisms of aging. The Sir2 catalytic domain, which is shared among all sirtuins, consists of two distinct domains that bind NAD and the acetyl-lysine substrate, respectively. In addition to the catalytic domain, eukaryotic sirtuins contain variable amino- and carboxy-terminal extensions that regulate their subcellular localizations and catalytic activity.

Functional diversity of silencers in budding yeasts

We studied the silencing of the cryptic mating-type loci HMLa and HMRa in the budding yeast Kluyveromyces lactis. A 102-bp minimal silencer fragment was defined that was both necessary and sufficient for silencing of HMLalpha. Mutagenesis of the silencer revealed three distinct regions (A, B, and C) that were important for silencing. Recombinant K. lactis ribosomal DNA enhancer binding protein 1 (Reb1p) could bind the silencer in vitro, and point mutations in the B box abolished both Reb1p binding and silencer function. Furthermore, strains carrying temperature-sensitive alleles of the REBI gene derepressed the transcription of the HMLalpha1 gene at the nonpermissive temperature. A functional silencer element from the K. lactis cryptic HMRa locus was also identified, which contained both Reb1p binding sites and A boxes, strongly suggesting a general role for these sequences in K lactis silencing. Our data indicate that different proteins bind to Kluyveromyces silencers than to Saccharomyces silencers. We suggest that the evolution of silencers is rapid in budding yeasts and discuss the similarities and differences between silencers in Saccharomyces and Kluyveromyces.

Common themes in mechanisms of gene silencing

The assembly of DNA into regions of inaccessible chromatin, called silent chromatin, is involved in the regulation of gene expression and maintenance of chromosome stability in eukaryotes. Recent studies on Sir2-containing silencing complexes in budding yeast and HP1- and Swi6-containing silencing complexes in metazoans and fission yeast suggest a common mechanism for the assembly of these domains, which involves the physical coupling of histone modifying enzymes to histone binding proteins.

An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing

Despite its conservation in organisms from bacteria to human and its general requirement for transcriptional silencing in yeast, the function of the Sir2 protein is unknown. Here we show that Sir2 can transfer labeled phosphate from nicotinamide adenine dinucleotide to itself and histones in vitro. A modified form of Sir2, which results from its automodification activity, is specifically recognized by anti-mono-ADP-ribose antibodies, suggesting that Sir2 is an ADP-ribosyltransferase. Mutation of a phylogenetically invariant histidine residue in Sir2 abolishes both its enzymatic activity in vitro and its silencing functions in vivo. However, the mutant protein is associated with chromatin and other silencing factors in a manner similar to wild-type Sir2. These findings suggest that Sir2 contains an ADP-ribosyltransferase activity that is essential for its silencing function.

Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae has a limited life-span, which is measured by the number of divisions that individual cells complete. Among the many changes that occur as yeasts age are alterations in chromatin-dependent transcriptional silencing. We have genetically manipulated histone deacetylases to modify chromatin, and we have examined the effect on yeast longevity. Deletion of the histone deacetylase gene RPD3 extended life-span. Its effects on chromatin functional state were evidenced by enhanced silencing at the three known heterochromatic regions of the genome, the silent mating type (HM), subtelomeric, and rDNA loci, which occurred even in the absence of SIR3. Similarly, the effect of the rpd3Delta on life-span did not depend on an intact Sir silencing complex. In fact, deletion of SIR3 itself had little effect on life-span, although it markedly accelerated the increase in cell generation time that is observed during yeast aging. Deletion of HDA1, another histone deacetylase gene, did not result in life-span extension, unless it was combined with deletion of SIR3. The hda1Delta sir3Delta resulted in an increase in silencing, but only at the rDNA locus. Deletion of RPD3 suppressed the loss of silencing in rDNA in a sir2 mutant; however, the silencing did not reach the level found in the rpd3Delta single mutant, and RPD3 deletion did not overcome the life-span shortening seen in the sir2 mutant. Deletion of both RPD3 and HDA1 caused a decrease in life-span, which resulted from a substantial increase in initial mortality of the population. The expression of both of these genes declines with age, providing one possible explanation for the increase in mortality during the life-span. Our results are consistent with the loss of rDNA silencing leading to aging in yeast. The functions of RPD3 and HDA1 do not overlap entirely. RPD3 exerts its effect on chromatin at additional sites in the genome, raising the possibility that events at loci other than rDNA play a role in the aging process.

Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern

Heterochromatin in metazoans induces transcriptional silencing, as exemplified by position effect variegation in Drosophila melanogaster and X-chromosome inactivation in mammals. Heterochromatic DNA is packaged in nucleosomes that are distinct in their acetylation pattern from those present in euchromatin, although the role these differences play in the structure of heterochromatin or in the effects of heterochromatin on transcriptional activity is unclear. Here we report that, as observed in the facultative heterochromatin of the inactive X chromosome in female mammalian cells, histones H3 and H4 in chromatin spanning the transcriptionally silenced mating-type cassettes of the yeast Saccharomyces cerevisiae are hypoacetylated relative to histones H3 and H4 of transcriptionally active regions of the genome. By immunoprecipitation of chromatin fragments with antibodies specific for H4 acetylated at particular lysine residues, we found that only three of the four lysine residues in the amino-terminal domain of histone H4 spanning the silent cassettes are hypoacetylated. Lysine 12 shows significant acetylation levels. This is identical to the pattern of histone H4 acetylation observed in centric heterochromatin of D. melanogaster. These two observations provide additional evidence that the silent cassettes are encompassed in the yeast equivalent of metazoan heterochromatin. Further, mutational analysis of the amino-terminal domain of histone H4 in S. cerevisiae demonstrated that this observed pattern of histone H4 acetylation is required for transcriptional silencing. This result, in conjunction with prior mutational analyses of yeast histones H3 and H4, indicates that the particular pattern of nucleosome acetylation found in heterochromatin is required for its effects on transcription and is not simply a side effect of heterochromatin formation.

Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression

Transcriptional repression at the silent mating-type loci in yeast requires the targeting of silent information regulator (Sir) proteins through specific interactions formed at cis-acting silencer elements. We show here that a reporter gene flanked by two functional silencers is not repressed when integrated at >200 kb from a telomere. Repression is restored by creation of a new telomere 13 kb from the integrated reporter or by elevated expression of SIR1, SIR3, and/or SIR4. Coupled expression represses in an additive manner, suggesting that all three factors are in limiting concentrations. When overexpressed, Sir3 and Sir4 are dispersed throughout the nucleoplasm, in contrast to wild-type cells where they are clustered in a limited number of foci together with telomeres. Efficient silencer function thus seems to require either proximity to a pool of concentrated Sir proteins, that is, proximity to telomeres, or delocalization of the silencing factors.

A developmentally regulated position effect at a telomeric locus in Trypanosoma brucei

Trypanosoma brucei undergoes antigenic variation in the mammalian host. This can be achieved by activation and inactivation of telomeric variant-specific surface glycoprotein genes (vsg). In procyclic (insect midgut stage) cells, Vsg is not expressed. The mechanisms that regulate transcription of vsg expression sites (ESs) are unknown. Here we demonstrate that transcription from three different promoters was repressed when they were inserted at a transcriptionally silent telomere-proximal locus in bloodstream-form cells. This position effect was stable and heritable. Only transcription from an ES promoter was repressed in procyclic cells. The observed position effect and the promoter-specific developmental regulation suggest that these phenomena reflect the mechanisms that regulate vsg expression.

The homeobox gene ATK1 of Arabidopsis thaliana is expressed in the shoot apex of the seedling and in flowers and inflorescence stems of mature plants

The homeodomain is a DNA-binding domain present in a large family of eukaryotic regulatory proteins. Homeodomain proteins have been shown to play key roles in controlling developmental programs in various organisms. Here we report the isolation and characterisation of a homeobox gene from Arabidopsis thaliana designated ATK1. The gene was isolated using as a probe the homeobox domain of the KN1 gene from maize. The homeodomain of ATK1 is highly homologous to the homeodomain of the KN1 gene of maize (81%) but shows only poor homology outside the homeodomain. Therefore ATK1 is probably not the Arabidopsis homologue of the KN1 gene from maize. It contains the four invariant amino acid residues present in the recognition helix 3 of all other homeodomain proteins. Outside the homeodomain a region rich in aspartate and glutamate residues is found suggesting that ATK1 is a transcriptional activator. The gene contains four introns which is similar in the KN1 gene of maize and the Osh1 gene of rice. Primer extension reveals the presence of two transcription initiation sites. The leader sequence of the genuine transcript is 342 nucleotides long and contains two upstream open reading frames. ATK1 is strongly expressed in the shoot apex of seedlings, while in mature plants the gene is primarily expressed in flowers and inflorescence stems. Such an expression pattern is reminiscent of that of the KN1 gene of maize and therefore ATK1 could similarly be involved in determining cell fate.

Yeast silencers can act as orientation-dependent gene inactivation centers that respond to environmental signals

The mating-type loci located at the ends of chromosome III in Saccharomyces cerevisiae are transcriptionally repressed by a region-specific but sequence-nonspecific silencing apparatus, mediated by cis-acting silencer sequences. Previous deletion analyses have defined the locations and organizations of the silencers in their normal context and have shown that they are composed of various combinations of replication origins and binding sites for specific DNA-binding proteins. We have evaluated what organization of silencer sequences is sufficient for establishing silencing at a novel location, by inserting individual silencers next to the MAT locus and then assessing expression of MAT. The results of this analysis indicate that efficient silencing can be achieved by inserting either a single copy of the E silencer from HMR or multiple, tandem copies of either the E or I silencer from HML. These results indicate that while all silencers are functionally equivalent, they have different efficiencies; HMR E is more active than HML E, which itself is more active than HML I. Both HMR E and HML E exhibit orientation-dependent silencing, and the particular organization of binding elements within the silencer domain is critical for function. In some situations, silencing of MAT is conditional: complete silencing is obtained when cells are grown on glucose, and complete derepression occurs when cells are shifted to a nonfermentable carbon source, a process mediated in part by the RAS/cyclic AMP signaling pathway. Finally, the E silencer from HMR is able to reestablish repression immediately upon a shift back to glucose, while the silencers from HML exhibit a long lag in reestablishing repression, thus indicating distinctions between the two silencers in their reestablishment capacities. These results demonstrate that silencers can serve as nonspecific gene inactivation centers and that the attendant silencing can be rendered responsive to potential developmental cues.

Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast

RAP1 is a sequence-specific DNA-binding protein in yeast that can either repress or activate transcription. Previous studies have demonstrated a direct role for RAP1 in silencing at HM mating-type loci and telomeres. Here, we show that a small carboxy-terminal domain of RAP1 is sufficient to establish repression when fused to the GAL4 DNA-binding domain (GBD) and targeted to mutated HMR silencers containing GAL4 DNA-binding sites. Silencing by GBD/RAP1 hybrids, like normal silencing at HMR, requires the trans-acting factors SIR2, SIR3, and SIR4. However, GBD/RAP1-mediated silencing is independent of SIR1, whose product is normally required for the establishment of repression at HMR. Targeted silencing also displays an unusual response to silencing-defective rap1s mutations. The incorporation of a rap1s missense mutation into GBD/RAP1 hybrids can improve targeted silencing, yet wild-type GBD/RAP1 hybrids fail to establish repression in strains in which the endogenous RAP1 locus carries a rap1s mutation. In addition, we find that telomeric silencing is increased in rap1s strains. We propose that the rap1s mutation creates an HMR-specific silencing defect by shifting a balance between silencing at HMR and telomeres in favor of telomeric silencing. This balance is regulated by telomere length and by interactions between the RAP1 carboxyl terminus and both RIF1 and SIR4 proteins. In support of this model, we show that abnormally long telomeres antagonize silencing at HMR and a rap1s hybrid protein displays a strengthened interaction with SIR4 in a two-hybrid assay.

Fusion with E2A converts the Pbx1 homeodomain protein into a constitutive transcriptional activator in human leukemias carrying the t(1;19) translocation

E2A-PBX1 is a chimeric gene formed by the t(1;19)(q23;p13.3) chromosomal translocation of pediatric pre-B-cell leukemia. The E2A-Pbx1 fusion protein contains sequences encoding the transactivation domain of E2A joined to a majority of the Pbx1 protein, which contains a novel homeodomain. Earlier, we found that expression of E2A-Pbx1 causes malignant transformation of NIH 3T3 fibroblasts and induces myeloid leukemia in mice. Here we demonstrate that the homeodomains encoded by PBX1, as well as by the highly related PBX2 and PBX3 genes, bind the DNA sequence ATCAATCAA. E2A-Pbx1 strongly activates transcription in vivo through this motif, while Pbx1 does not. This finding suggests that E2A-Pbx1 transforms cells by constitutively activating transcription of genes regulated by Pbx1 or by other members of the Pbx protein family.

Fusion with E2A converts the Pbx1 homeodomain protein into a constitutive transcriptional activator in human leukemias carrying the t(1;19) translocation

E2A-PBX1 is a chimeric gene formed by the t(1;19)(q23;p13.3) chromosomal translocation of pediatric pre-B-cell leukemia. The E2A-Pbx1 fusion protein contains sequences encoding the transactivation domain of E2A joined to a majority of the Pbx1 protein, which contains a novel homeodomain. Earlier, we found that expression of E2A-Pbx1 causes malignant transformation of NIH 3T3 fibroblasts and induces myeloid leukemia in mice. Here we demonstrate that the homeodomains encoded by PBX1, as well as by the highly related PBX2 and PBX3 genes, bind the DNA sequence ATCAATCAA. E2A-Pbx1 strongly activates transcription in vivo through this motif, while Pbx1 does not. This finding suggests that E2A-Pbx1 transforms cells by constitutively activating transcription of genes regulated by Pbx1 or by other members of the Pbx protein family.

Homeobox-containing genes in the most primitive metazoa, the sponges

The porifera represent the most primitive phylum of the metazoa. We identified three homeobox-containing genes in the freshwater sponge (Ephydatia fluviatilis). Genomic DNA of the sponge was subjected to amplification by PCR with two primers that corresponded to the helix-1 and helix-3 regions of the homeodomain. Using the amplified products as probes, we isolated two homeobox genes, designated prox1 and prox2. The amino acid sequences of the homeodomains of prox1 and prox2 were 72% and 62% identical to those of the NK-3 and Om(1D) genes of Drosophila, respectively. Screening of a sponge genomic library with degenerate oligonucleotides that corresponded to helix 3 further revealed the presence of one more homeobox gene, prox3. The amino acid sequence of the homeodomain of the prox3 product was 77% identical to that of the msh gene product of human. These results indicate that, when the metazoa appeared during the course of evolution, the multiple and distinct classes of homeobox-containing genes that have been identified in higher organisms already existed.

Identification of a homeobox-containing gene with enhanced expression during soybean (Glycine max L.) somatic embryo development

Homeotic gene are key 'switches' that control developmental processes. Homeotic genes containing the consensus 'homeobox' domain have been identified from a number of organisms including Drosophila melanogaster, Caenorhabditis elegans, Homo sapiens, and Zea mays. Although homeotic genes have been demonstrated to be important in embryo development of some insects, amphibians, and mammals, there are no reports of their involvement in plant embryogenesis. Here, we report the isolation and characterization of a cDNA clone for a homeobox-containing gene expressed in somatic embryos of soybean. The cDNA (Sbh1 for soybean homeobox-containing gene) was isolated using maize Knotted-1 (Kn1) cDNA as a heterologous probe. The Sbh1 cDNA clone is 1515 bp long which is the approximate size of its transcript. Within the homeodomain, the amino acid sequence of a helix-turn-helix structure, and invariant and conserved residues were identified. The deduced SBH1 protein shares a high amino acid identity with KN1 protein (47.0% overall and 87.5% for the homeodomain). Southern hybridization analysis indicated that Sbh1 is a member of a small gene family. The expression of Sbh1 is development- and tissue-specific. The transcript of Sbh1 was present in early-stage somatic embryos, increased prior to cotyledon formation and decreased thereafter. Sbh1 was weakly expressed in soybean stems and hypocotyl but was not detected in other plant tissues and nonembryogenic materials. The enhanced expression during embryogenesis, the homology with maize Kn1 gene, and the regulatory nature of homeodomain proteins suggest that the SBH1 protein plays an important role in plant embryo development.

Specific repression of the yeast silent mating locus HMR by an adjacent telomere

The yeast silent mating loci HML and HMR are located at opposite ends of chromosome III adjacent to the telomeres. Mutations in the N terminus of histone H4 have been previously found to derepress the yeast silent mating locus HML to a much greater extent than HMR. Although differences in the a and alpha mating-type regulatory genes and in the cis-acting silencer elements do not appear to strongly influence the level of derepression at HMR, we have found that the differential between the two silent cassettes is largely due to the position of the HMR cassette relative to the telomere on chromosome III. While HML is derepressed to roughly the same extent by mutations in histone H4 regardless of its chromosomal location, HMR is affected to different extends depending upon its chromosomal positioning. We have found that HMR is more severely derepressed by histone H4 mutations when positioned far from the telomere (cdc14 locus on chromosome VI) but is only minimally affected by the same mutations when integrated immediately adjacent to another telomere (ADH4 locus on chromosome VII). These data indicate that the degree of silencing at HMR is regulated in part by its neighboring telomere over a distance of at least 23 kb and that this form of regulation is unique for HMR and not present at HML. These data also indicate that histone H4 plays an important role in regulating the silenced state at both HML and HMR.

Position effect variegation at fission yeast centromeres

Chromatin structure at Schizosaccharomyces pombe centromeres is unusual. The insertion of the ura4 gene within these centromeres resulted in genetically identical cells mosaic for its expression. Placement of the ade6 gene within cen1 or cen3 resulted in red-white sectored colonies, demonstrating the instability of gene expression. The occurrence of pink colonies implied that intermediate levels of repression were established. Repression of both genes within centromeres was temperature sensitive. The chromatin structure of the ura4 gene at centromeres was altered, suggesting that the unusual chromatin encroaches into the gene and inhibits normal expression. These repressive effects at S. pombe centromeres resemble the classical phenomenon of position effect variegation imposed by Drosophila heterochromatin on nearby genes. However, since the epigenetic states can be set at intermediate levels of expression, a purely euchromatin-heterochromatin dichotomy does not apply. A model for the epigenetic regulation of genes placed within S. pombe centromeres is presented.

Isolation of silencer-containing sequences causing a tissue-specific position effect on alcohol dehydrogenase expression in Drosophila melanogaster

A transient expression assay has been used to investigate the cause of a tissue-specific position effect on Adh expression from a transgene insertion in Drosophila. A 15.4-kb genomic clone containing the 3.2-kb Adh insert along with flanking regions of genomic DNA is expressed in this assay in a tissue-specific pattern resembling the abnormal expression pattern of the position effect. The 3.2-kb Adh insert is expressed normally without the flanking sequences. A silencer element is located upstream of the Adh gene within a 2-kb fragment that acts in both orientations and at a distance of at least 6.5 kb from the larval Adh promoter to suppress ADH expression in a nontissue specific fashion. The DNA sequence of the 2-kb fragment indicates that it is a noncoding region. A 17-bp sequence is repeated within this region and may be associated with the silencer activity, since subclones from the 2-kb fragment, each containing one of the repeated regions, both retain full silencer activity. This silencer fails to suppress expression from an alpha 1-tubulin promoter-LacZ fusion construct or an hsp70 promoter-Adh fusion construct. In addition to the silencer, another element is located downstream of the Adh gene that produces a higher level of anterior than posterior midgut expression. These results suggest that the 5' silencer and the 3' element act together to create the tissue specific position effect characteristic of the GC-1 line.

Specific repression of the yeast silent mating locus HMR by an adjacent telomere

The yeast silent mating loci HML and HMR are located at opposite ends of chromosome III adjacent to the telomeres. Mutations in the N terminus of histone H4 have been previously found to derepress the yeast silent mating locus HML to a much greater extent than HMR. Although differences in the a and alpha mating-type regulatory genes and in the cis-acting silencer elements do not appear to strongly influence the level of derepression at HMR, we have found that the differential between the two silent cassettes is largely due to the position of the HMR cassette relative to the telomere on chromosome III. While HML is derepressed to roughly the same extent by mutations in histone H4 regardless of its chromosomal location, HMR is affected to different extends depending upon its chromosomal positioning. We have found that HMR is more severely derepressed by histone H4 mutations when positioned far from the telomere (cdc14 locus on chromosome VI) but is only minimally affected by the same mutations when integrated immediately adjacent to another telomere (ADH4 locus on chromosome VII). These data indicate that the degree of silencing at HMR is regulated in part by its neighboring telomere over a distance of at least 23 kb and that this form of regulation is unique for HMR and not present at HML. These data also indicate that histone H4 plays an important role in regulating the silenced state at both HML and HMR.

The yeast alpha 2 protein can repress transcription by RNA polymerases I and II but not III

The alpha 2 protein of the yeast Saccharomyces cerevisiae normally represses a set of cell-type-specific genes (the a-specific genes) that are transcribed by RNA polymerase II. In this study, we determined whether alpha 2 can affect transcription by other RNA polymerases. We find that alpha 2 can repress transcription by RNA polymerase I but not by RNA polymerase III. Additional experiments indicate that alpha 2 represses RNA polymerase I transcription through the same pathway that it uses to repress RNA polymerase II transcription. These results implicate conserved components of the transcription machinery as mediators of alpha 2 repression and exclude several alternate models.

The yeast alpha 2 protein can repress transcription by RNA polymerases I and II but not III

The alpha 2 protein of the yeast Saccharomyces cerevisiae normally represses a set of cell-type-specific genes (the a-specific genes) that are transcribed by RNA polymerase II. In this study, we determined whether alpha 2 can affect transcription by other RNA polymerases. We find that alpha 2 can repress transcription by RNA polymerase I but not by RNA polymerase III. Additional experiments indicate that alpha 2 represses RNA polymerase I transcription through the same pathway that it uses to repress RNA polymerase II transcription. These results implicate conserved components of the transcription machinery as mediators of alpha 2 repression and exclude several alternate models.

Transcriptional silencing in yeast is associated with reduced nucleosome acetylation

Two classes of sequences in the yeast Saccharomyces cerevisiae are subject to transcriptional silencing: the silent mating-type cassettes and telomeres. In this report we demonstrate that the silencing of these regions is strictly associated with acetylation of the epsilon-amino groups of lysines in the amino-terminal domains of three of the four core histones. Both the silent mating-type cassettes and the Y domains of telomeres are packaged in nucleosomes in vivo that are hypoacetylated relative to those packaging active genes. This difference in acetylation is eliminated by genetic inactivation of silencing: The silent cassettes from sir2, sir3, or sir4 cells show the same level of acetylation as other active genes. The correspondence of silencing and hypoacetylation of the mating-type cassettes is observed even for an allele lacking a promoter, indicating that silencing per se, rather than the absence of transcription, is correlated with hypoacetylation. Finally, overexpression of Sir2p, a protein required for transcriptional silencing in yeast, yields substantial histone deacetylation in vivo. These studies fortify the hypothesis that silencing in yeast results from heterochromatin formation and argue that the silencing proteins participate in this formation.

Conditional silencing: the HMRE mating-type silencer exerts a rapidly reversible position effect on the yeast HSP82 heat shock gene

The HMRE silencer of Saccharomyces cerevisiae has been previously shown to transcriptionally repress class II and class III genes integrated within the HMR silent mating-type locus up to 2.6 kb away. Here we study the ability of this element to repress at an ectopic position, independent of sequences normally associated with it. When integrated 750 bp upstream of the HSP82 heat shock gene, the silencer represses basal-level transcription approximately 5-fold but has no effect on chemical- or heat-shock-induced expression. Such conditional silencing is also seen when the HMRE/HSP82 allele is carried on a centromeric episome or when the entire HMRa domain is transplaced 2.7 kb upstream of HSP82. Notably, the a1 promoter within the immigrant HMRa locus remains fully repressed at the same time HSP82 is derepressed. The position effect mediated by the E silencer is absolutely dependent on the presence of a functional SIR4 gene product, is lost within 1 min following stress induction, and is fully reestablished within 15 min following a return to nonstressful conditions. Similar kinetics of reestablishment are seen in HMRE/HSP82 and HMRa/HSP82 strains, indicating that complete repression can be mediated over thousands of base pairs within minutes. DNase I chromatin mapping reveals that the ABF1, RAP1, and autonomously replicating sequence factor binding sites within the silencer are constitutively occupied in chromatin, unaltered by heat shock or the presence of SIR4. Similarly, the heat shock factor binding site upstream of HSP82 remains occupied under such conditions, suggesting concurrent occupancy of silencer and activator binding sites. Our results are consistent with a model in which silencing at the HMRE/HSP82 allele is mediated by direct or indirect contacts between the silencer protein complex and heat shock factor.

Conditional silencing: the HMRE mating-type silencer exerts a rapidly reversible position effect on the yeast HSP82 heat shock gene

The HMRE silencer of Saccharomyces cerevisiae has been previously shown to transcriptionally repress class II and class III genes integrated within the HMR silent mating-type locus up to 2.6 kb away. Here we study the ability of this element to repress at an ectopic position, independent of sequences normally associated with it. When integrated 750 bp upstream of the HSP82 heat shock gene, the silencer represses basal-level transcription approximately 5-fold but has no effect on chemical- or heat-shock-induced expression. Such conditional silencing is also seen when the HMRE/HSP82 allele is carried on a centromeric episome or when the entire HMRa domain is transplaced 2.7 kb upstream of HSP82. Notably, the a1 promoter within the immigrant HMRa locus remains fully repressed at the same time HSP82 is derepressed. The position effect mediated by the E silencer is absolutely dependent on the presence of a functional SIR4 gene product, is lost within 1 min following stress induction, and is fully reestablished within 15 min following a return to nonstressful conditions. Similar kinetics of reestablishment are seen in HMRE/HSP82 and HMRa/HSP82 strains, indicating that complete repression can be mediated over thousands of base pairs within minutes. DNase I chromatin mapping reveals that the ABF1, RAP1, and autonomously replicating sequence factor binding sites within the silencer are constitutively occupied in chromatin, unaltered by heat shock or the presence of SIR4. Similarly, the heat shock factor binding site upstream of HSP82 remains occupied under such conditions, suggesting concurrent occupancy of silencer and activator binding sites. Our results are consistent with a model in which silencing at the HMRE/HSP82 allele is mediated by direct or indirect contacts between the silencer protein complex and heat shock factor.

Silencers, silencing, and heritable transcriptional states

Three copies of the mating-type genes, which determine cell type, are found in the budding yeast Saccharomyces cerevisiae. The copy at the MAT locus is transcriptionally active, whereas identical copies of the mating-type genes at the HML and HMR loci are transcriptionally silent. Hence, HML and HMR, also known as the silent mating-type loci, are subject to a position effect. Regulatory sequences flank the silent mating-type loci and mediate repression of HML and HMR. These regulatory sequences are called silencers for their ability to repress the transcription of nearby genes in a distance- and orientation-independent fashion. In addition, a number of proteins, including the four SIR proteins, histone H4, and an alpha-acetyltransferase, are required for the complete repression of HML and HMR. Because alterations in the amino-terminal domain of histone H4 result in the derepression of the silent mating-type loci, the mechanism of repression may involve the assembly of a specific chromatin structure. A number of additional clues permit insight into the nature of repression at HML and HMR. First, an S phase event is required for the establishment of repression. Second, at least one gene appears to play a role in the establishment mechanism yet is not essential for the stable propagation of repression through many rounds of cell division. Third, certain aspects of repression are linked to aspects of replication. The silent mating-type loci share many similarities with heterochromatin. Furthermore, regions of S. cerevisiae chromosomes, such as telomeres, which are known to be heterochromatic in other organisms, require a subset of SIR proteins for repression. Further analysis of the transcriptional repression at the silent mating-type loci may lend insight into heritable repression in other eukaryotes.

An origin of DNA replication and a transcription silencer require a common element

A eukaryotic chromosomal origin of replication was identified in the yeast Saccharomyces cerevisiae. By several criteria, including map position, deletion analysis, and a synthetic form of saturation mutagenesis, the origin co-localized with the HMR-E silencer, which is a DNA element that represses transcription of the adjacent genes. A specific site within the silencer was required for both initiation of chromosomal replication and for repression of transcription. This analysis directly demonstrates that initiation of eukaryotic chromosomal replication is dependent on specific sequence elements and that a particular element can act in both initiation of chromosomal replication and regulation of transcription.

Silencing: the establishment and inheritance of stable, repressed transcription states

Silencing refers to a particular type of transcriptional repression characterized by the formation of a genetically heritable, repressed transcriptional state. Examples of silencing include position-effect variegation, X-chromosome inactivation, and the repression of the silent mating-type gene loci in yeast. Recent discoveries suggest that silencing in yeast, like silencing in larger eukaryotes, results from a particular chromatin structure that defines a chromosomal domain. In addition, a chromosomal origin of DNA replication is required for silencing in yeast, suggesting that DNA replication plays a role in forming functional chromosomal domains.

Cloning of the Drosophila prospero gene and its expression in ganglion mother cells

The Drosophila central nervous system comprises an enormous diversity of neurons that are originated from neuronal stem cells, neuroblasts. They generate a specific series of ganglion mother cells, each of which is once cleaved into a pair of neurons. Among genes known to control neurogenesis, prospero (pros) was recently identified as a gene required for gene expression specifying properties of some identified neurons. Here we report that pros encodes a nuclear protein containing a homeodomain-like sequence. In neuronal lineages of the central nervous system, pros protein is specifically detected in ganglion mother cells, although their parental neuroblasts have begun expressing a significant level of pros transcripts, suggesting a post-transcriptional control of pros expression. Our results provoke that in neuronal cell differentiation ganglion mother cells might play a pivotal role associating with the pros function.

A synthetic silencer mediates SIR-dependent functions in Saccharomyces cerevisiae

Copies of the mating-type genes are present at three loci on chromosome III of the yeast Saccharomyces cerevisiae. The genes at the MAT locus are transcribed, whereas the identical genes at the silent loci, HML and HMR, are not transcribed. Several genes, including the four SIR genes, and two sites, HMR-E and HMR-I, are required for repression of transcription at the HMR locus. Three elements have been implicated in the function of the HMR-E silencer: a binding site for the RAP1 protein, a binding site for the ABF1 protein, and an 11-bp consensus sequence common to nearly all autonomously replicating sequence (ARS) elements (putative origins of DNA replication). RAP1 and ABF1 binding sites of different sequence than those found at HMR-E were joined with an 11-bp ARS consensus sequence to form a synthetic silencer. The synthetic silencer was able to repress transcription of the HMRa1 gene, confirming that binding sites for RAP1 and ABF1 and the 11-bp ARS consensus sequence were the functional components of the silencer in vivo. Mutations in the ABF1 binding site or in the ARS consensus sequence of the synthetic silencer caused nearly complete derepression of transcription at HMR. The ARS consensus sequence mutation also eliminated the ARS activity of the synthetic silencer. These data suggested that replication initiation at the HMR-E silencer was required for establishment of the repressed state at the HMR locus.

A synthetic silencer mediates SIR-dependent functions in Saccharomyces cerevisiae

Copies of the mating-type genes are present at three loci on chromosome III of the yeast Saccharomyces cerevisiae. The genes at the MAT locus are transcribed, whereas the identical genes at the silent loci, HML and HMR, are not transcribed. Several genes, including the four SIR genes, and two sites, HMR-E and HMR-I, are required for repression of transcription at the HMR locus. Three elements have been implicated in the function of the HMR-E silencer: a binding site for the RAP1 protein, a binding site for the ABF1 protein, and an 11-bp consensus sequence common to nearly all autonomously replicating sequence (ARS) elements (putative origins of DNA replication). RAP1 and ABF1 binding sites of different sequence than those found at HMR-E were joined with an 11-bp ARS consensus sequence to form a synthetic silencer. The synthetic silencer was able to repress transcription of the HMRa1 gene, confirming that binding sites for RAP1 and ABF1 and the 11-bp ARS consensus sequence were the functional components of the silencer in vivo. Mutations in the ABF1 binding site or in the ARS consensus sequence of the synthetic silencer caused nearly complete derepression of transcription at HMR. The ARS consensus sequence mutation also eliminated the ARS activity of the synthetic silencer. These data suggested that replication initiation at the HMR-E silencer was required for establishment of the repressed state at the HMR locus.

Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae

Genes placed near telomeres in S. cerevisiae succumb to position-effect variegation. SIR2, SIR3, SIR4, NAT1, ARD1, and HHF2 (histone H4) were identified as modifiers of the position effect at telomeres, since transcriptional repression near telomeres was no longer observed when any of the modifier genes were mutated. These genes, in addition to SIR1, have previously been shown to repress transcription at the silent mating loci, HML and HMR. However, there were differences between transcriptional silencing at telomeres and the HM loci, as demonstrated by suppressor analysis and the lack of involvement of SIR1 in telomeric silencing. These findings provide insights into telomeric structure and function that are likely to apply to many eukaryotes. In addition, the distinctions between telomeres and the HM loci suggest a hierarchy of chromosomal silencing in S. cerevisiae.

Mutations in the HML E silencer of Saccharomyces cerevisiae yield metastable inheritance of transcriptional repression

Mating-type genes resident in the silent cassette HML at the left arm of chromosome III are repressed by the action of four SIR gene products, mediated independently through two cis-acting sites, termed the E and I silencers. We have found that in the absence of the I silencer, deletion of any one of three distinct elements within E yields partial derepression of the mating-type genes resident at HML, whereas deletion of any two yields full derepression. These elements correspond to a binding site for the abundant DNA-binding protein RAP1, an autonomous replicating sequence (ARS), and an as yet undistinguished region. From detailed deletion analysis of the E site we conclude that the ARS element contributes to silencer function in a capacity distinct from its role as an initiator of DNA replication. In addition, we find that strains deleted for any one of these elements comprise two genetically identical but phenotypically distinct types of cells: Those with HML apparently fully derepressed, and those with HML apparently completely repressed. These results reinforce the notion that epigenetic inheritance is an intrinsic characteristic of silencer action.

Neurospora crassa A mating-type region

The mating-type locus of the haploid filamentous fungus Neurospora crassa is a regulatory region that controls entry into the sexual cycle and prevents formation of mixed mating-type heterokaryons in the vegetative phase. The locus consists of alternative sequences called A and a. The A mating-type DNA sequence of Neurospora crassa is composed of a region of 5301 base pairs that has little similarity to the sequence present at the mating-type locus in an a mating-type strain. However, the sequences flanking the mating-type locus in the A haploid and a haploid genome are essentially identical. The region of the A mating-type sequence required for expression of the heterokaryon incompatibility and sexual functions has been localized to a single open reading frame (ORF) encoding a polypeptide of 288 amino acids. Sequence analysis of sterile, heterokaryon-compatible mutants reveals frameshift mutations in this same ORF. The putative 288-amino acid product has a region of similarity to the MAT alpha 1 polypeptide of Saccharomyces cerevisiae.