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Martens, J.A., P.Y. Wu, and F. Winston (2005) Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev. 19:2695-2704 Recent studies have revealed that transcription of noncoding, intergenic DNA is abundant among eukaryotes. However, the functions of this transcription are poorly understood. We have previously shown that in Saccharomyces cerevisiae, expression of an intergenic transcript, SRG1, represses the transcription of the adjacent gene, SER3, by transcription interference. We now show that SRG1 transcription is regulated by serine, thereby conferring regulation of SER3, a serine biosynthetic gene. This regulation requires Cha4, a serine-dependent activator that binds to the SRG1 promoter and is required for SRG1 induction in the presence of serine. Furthermore, two coactivator complexes, SAGA and Swi/Snf, are also directly required for activation of SRG1 and transcription interference of SER3. Taken together, our results elucidate a physiological role for intergenic transcription in the regulation of SER3. Moreover, our results demonstrate a mechanism by which intergenic transcription allows activators to act indirectly as repressors.
Martens, J.A., L. Laprade, and F. Winston (2004) Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429:571-574 Transcription by RNA polymerase II in Saccharomyces cerevisiae and in humans is widespread, even in genomic regions that do not encode proteins. The purpose of such intergenic transcription is largely unknown, although it can be regulatory. We have discovered a role for one case of intergenic transcription by studying the S. cerevisiae SER3 gene. Our previous results demonstrated that transcription of SER3 is tightly repressed during growth in rich medium. We now show that the regulatory region of this gene is highly transcribed under these conditions and produces a non-protein-coding RNA (SRG1). Expression of the SRG1 RNA is required for repression of SER3. Additional experiments have demonstrated that repression occurs by a transcription-interference mechanism in which SRG1 transcription across the SER3 promoter interferes with the binding of activators. This work identifies a previously unknown class of transcriptional regulatory genes.
Martens, J.A., and F. Winston (2003) Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev. 13:136-142 Members of the Swi/Snf family of chromatin-remodeling complexes play critical roles in transcriptional control. Recent studies have made significant advances in our understanding of the fundamental aspects of Swi/Snf complexes, including the roles of specific subunits, the repression of transcription, and the mechanism of remodeling. In addition, new findings also indicate an important role for the Swi/Snf-related complex, RSC, in controlling gene expression.
Martens, J.A., and F. Winston (2002) Evidence that Swi/Snf directly represses transcription in S. cerevisiae. Genes Dev. 16:2231-2236 Many studies have established that the Swi/Snf family of chromatin-remodeling complexes activate transcription. Recent reports have suggested the possibility that these complexes can also repress transcription. We now present chromatin immunoprecipitation evidence that the Swi/Snf complex of Saccharomyces cerevisiae directly represses transcription of the SER3 gene. Consistent with its role in nucleosome remodeling, Swi/Snf controls the chromatin structure of the SER3 promoter. However, in striking contrast to activation by Swi/Snf, which requires most Swi/Snf subunits, repression by Swi/Snf at SER3 is dependent primarily on one Swi/Snf component, Snf2. These results show distinct differences in the requirements for Swi/Snf components in transcriptional activation and repression.
Saleh, A., M. Collart, J.A. Martens, J. Genereaux, S. Allard, J. Cote, and C.J. Brandl (1998) TOM1p, a yeast hect-domain protein which mediates transcriptional regulation through the ADA/SAGA coactivator complexes. J. Mol. Biol. 282:933-946 The hect-domain has been characterized as a conserved feature of a group of E3 ubiquitin ligases. Here we show that the yeast hect-domain protein TOM1p regulates transcriptional activation through effects on the ADA transcriptional coactivator proteins. Null mutations of tom1 result in similar defects in transcription from ADH2 and HIS3 promoters, and enhanced transcription from the GAL10 promoter as do null mutations in ngg1/ada3. Strains with disruptions of both ngg1 and tom1 have the same phenotype as strains with a disruption of only ngg1 implying that these genes are acting through the same pathway. In the absence of TOM1p, the normal associations of the ADA proteins with SPT3p and the TATA-binding protein are reduced. The action of TOM1p is most likely mediated through ubiquitination since mutation of Cys3235 to Ala, corresponding residues of which are required for thioester bond formation with ubiquitin in other hect-domain proteins, results in similar changes in transcription as the null mutation. A direct role for TOM1p in regulation of ADA-associated proteins is further supported by the finding that SPT7p is ubiquitinated in a TOM1p-dependent fashion and that TOM1p coimmunoprecipitates with the ADA proteins.
Brandl, C.J., J.A. Martens, A. Margaliot, D. Stenning, A.M. Furlanetto, A. Saleh, K.S. Hamilton, and J. Genereaux (1996) Structure/functional properties of the yeast dual regulator protein NGG1 that are required for glucose repression. J. Biol. Chem. 271:9298-9306 NGG1p/ADA3p is a yeast dual function regulator required for the complete glucose repression of GAL4p-activated genes (Brandl, C. J., Furlanetto, A. M., Martens, J. A., and Hamilton, K. S. (1993) EMBO J. 12, 5255-5265). Evidence for a direct role for NGG1p in regulating activator function is supported by the finding that NGG1p is also required for transcriptional activation by GAL4p-VPl6 and LexA-GCN4p (Pina, B., Berger, S. L., Marcus, G. A., Silverman, N., Agapite, J., and Guarente, L. (1993) Mol. Cell. Biol. 13, 5981-5989). By analyzing deletion derivatives of the 702-amino acid protein, we identified a region essential for glucose repression within residues 274-373. Essential sequences were further localized to a segment rich in Phe residues that is predicted to be an amphipathic alpha helix. As well as finding mutations within this region that reduced glucose repression, we identified mutations that made NGG1p a better repressor. In addition, NGG1p probably represses GAL4p activity as part of a complex containing ADA2p because single and double disruptions of ngg1 and ada2 had comparable effects on glucose repression. We also localized a transcriptional activation domain within the amino-terminal amino acids of NGG1p that is proximal or overlapping the region required for glucose repression. Activation by GAL4p-NGG1p(1-373) requires ADA2p; however, activation by GAL4p-NGG1p(1-308), is ADA2p-independent. This suggests that a site required for ADA2p interaction lies between amino acids 308 and 373 and that ADA2p has a regulatory role in activation by GAL4p-NGG1p(1-373).
Martens, J.A., J. Genereaux, A. Saleh, and C.J. Brandl (1996) Transcriptional activation by yeast PDR1p is inhibited by its association with NGG1p/ADA3p. J. Biol. Chem. 271:15884-15890 NGG1p/ADA3p forms a coactivator/repressor complex (ADA complex) in association with at least two other yeast proteins, ADA2p and GCN5p, that is involved in regulating transcriptional activator proteins including GAL4p and GCN4p. Using a two-hybrid analysis, we found that the carboxyl-terminal transcriptional activation domain of PDR1p, the primary regulatory protein involved in yeast pleiotropic drug resistance, interacts with the amino-terminal 373 amino acids of NGG1p (NGG1p1-373). This interaction was confirmed by coimmunoprecipitation of epitope-tagged derivatives of NGG1p and PDR1p from crude extracts. An overlapping region of the related transcriptional activator PDR3p was also found to interact with NGG1p. Amino acids 274-307 of NGG1p were required for interaction with PDR1p. This same region is required for inhibition of transcriptional activation by GAL4p. The association between NGG1p1-373 and PDR1p may be indirect, possibly mediated by the ADA complex since the two-hybrid interaction required the presence of full-length NGG1. A partial requirement for ADA2 was also found. This suggests that an additional component of the ADA complex, regulated by ADA2p, may mediate the interaction. Transcriptional activation by a GAL4p DNA binding domain fusion of PDR1p was enhanced in ngg1 and ada2 disruption strains. Similar to its action on GAL4p, the ADA complex acts to inhibit the activation domain of PDR1p.
Martens, J.A., and C.J. Brandl (1994) GCN4p activation of the yeast TRP3 gene is enhanced by ABF1p and uses a suboptimal TATA element. J. Biol. Chem. 269:15661-15667 Transcription of the TRP3 gene of Saccharomyces cerevisiae is regulated by GCN4p from a position proximal to the transcriptional initiation sites. The promoter's apparent lack of a conventional TATA element sequence has led it to be used as a model for TATA-less promoters. Through mutational analysis of the TRP3 promoter, we have identified two additional regulatory elements required for expression. The first, located 57 base pairs (bp) upstream of the GCN4p binding site, binds ABF1p in vitro. The ABF1p binding site was required for maximal levels of GCN4p-activated transcription in vivo; however, the -fold activation by GCN4p was not altered by ABF1p. The second element, positioned 23 bp downstream of the GCN4p binding site, contained the TATA-like sequence, TATTAA. This element was required for both basal and activated expression and almost certainly functions as a TATA-binding protein interaction site. Mutations that improved its TATA character for native or an altered specificity mutant of TATA-binding protein correspondingly improved its function. Interestingly, basal expression induced by ABF1p was virtually unchanged in the presence of point mutations in the TATTAA element. Furthermore, unlike the case for HIS3 where only a limited subset of TATA-like sequences can activate transcription in conjunction with GCN4p, many divergent TATA-like sequences allowed GCN4p activation of TRP3. We suggest that the apparent promoter specific use of these TATA elements by GCN4p results from ABF1p amplifying the GCN4p-induced expression to a detectable level.
Brandl, C.J., A.M. Furlanetto, J.A. Martens, and K.S. Hamilton (1993) Characterization of NGG1, a novel yeast gene required for glucose repression of GAL4p-regulated transcription. EMBO J. 12:5255-5265 The GAL1-10 genes of Saccharomyces cerevisiae are regulated by the interaction of cis- and trans-acting factors which facilitate activated transcription in galactose but not in glucose medium. By selecting mutations that allow expression of a defective gal1-10-his3 hybrid promoter, we have identified a novel gene, NGG1, which is required for glucose repression of the GAL10-related his3-G25 promoter. ngg1 was identified as a recessive null mutation that in the presence of a gal80 background resulted in a 300-fold relief of glucose repression for the his3-G25 promoter. This compared with a 20-fold and negligible relief of repression in gal80 and ngg1 strains, respectively. Deletion analysis of the his3-G25 promoter showed a correlation between the number of GAL4p binding sites and the relative level of NGG1p activity. Relief of glucose repression by NGG1 was dependent on the presence of GAL4, but was independent of the GAL4 promoter. In addition, NGG1p activity was seen for a promoter construct containing independent GAL4p binding sites. These results suggest that NGG1p acts to inhibit GAL4p function in glucose medium. We have cloned NGG1 by complementation and found that it contains an open reading frame of 2106 bp which could encode a protein with a molecular weight of 79,230.
Brandl, C.J., J.A. Martens, P.C. Liaw, A.M. Furlanetto, and C.R. Wobbe (1992) TATA-binding protein activates transcription when upstream of a GCN4-binding site in a novel yeast promoter. J. Biol. Chem. 267:20943-20952 In the gal-his3 hybrid promoter, his3-GG1, GCN4 stimulates transcription at the position normally occupied by a TATA element. This expression requires two elements within gal1-10 sequences, a REB1-binding site and a second element, Z, which resides 20 base pairs upstream of the GCN4-binding site. No obvious TATA element is present in this promoter. To characterize the function of Z, we replaced it with short random oligonucleotides and selected for expression in vivo. Fourteen elements were identified and classified into groups based upon sequence and phenotypic similarities. Group 1 elements contained functional TATA sequences that were essential for activity. TATA elements can thus function when positioned upstream of a GCN4-binding site. The Group 2 elements activated transcription poorly when used as conventional TATA elements; however, mutational analyses demonstrated that their activity required TATA-like sequences. These TATA-like sequences bound the yeast TATA-binding protein (TBP) poorly in vitro but function in vivo as TBP interaction sites based upon two criteria. First mutations that improved their TATA character correspondingly improved function and second their activity could be enhanced in the presence of an altered binding specificity mutant of TBP. Furthermore, the Group 2 elements enabled the identification of mutations outside of the TATA-like core that contribute to transcriptional activation without adversely affecting TBP binding. The finding that low affinity TBP-binding sites can be used at unconventional positions suggests that many "TATA-less" promoters contain a cryptic interaction site for TBP.
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