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.

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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.

Transcription of non-protein-coding DNA (ncDNA) and its noncoding RNA (ncRNA) products are beginning to emerge as key regulators of gene expression. We previously identified a regulatory system in Saccharomyces cerevisiae whereby transcription of intergenic ncDNA (SRG1) represses transcription of an adjacent proteincoding gene (SER3) through transcription interference. We now provide evidence that SRG1 transcription causes repression of SER3 by directing a high level of nucleosomes over SRG1, which overlaps the SER3 promoter. Repression by SRG1 transcription is dependent on the Spt6 and Spt16 transcription elongation factors. Significantly, spt6 and spt16 mutations reduce nucleosome levels over the SER3 promoter without reducing intergenic SRG1 transcription, strongly suggesting that nucleosome levels, not transcription levels, cause SER3 repression. Finally, we show that spt6 and spt16 mutations allow transcription factor access to the SER3 promoter. Our results raise the possibility that transcription of ncDNA may contribute to nucleosome positioning on a genome-wide scale where, in some cases, it negatively impacts protein-DNA interactions.

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. The Saccharomyces cerevisiae Swi/Snf complex is the founding member of a large family of ATP-dependent chromatin-remodeling complexes that have been well characterized as transcriptional activators Vignali et al. 2000;Narlikar et al. 2002). Genetic and biochemical studies from both yeast and humans have provided strong evidence that Swi/Snf complexes can be recruited to the promoters of specific genes (Peterson and Workman 2000). Once at a promoter, these complexes can remodel nucleosomes to facilitate the binding of transcription factors to their sites on nucleosomal DNA (Peterson and Workman 2000;Vignali et al. 2000).In addition to their roles as transcriptional activators, several studies have suggested that Swi/Snf complexes serve as transcriptional repressors (Sudarsanam and Winston 2000; Urnov and Wolffe 2001). This idea arose both from studies of specific genes and from whole-genome expression analyses (for review, see Sudarsanam and Winston 2000; see also Angus-Hill et al. 2001). In addition, biochemical experiments have shown that Swi/Snf complexes can remodel nucleosomes in both directions between an inactive and a remodeled state (Lorch et al. 1998;Schnitzler et al. 1998). Although these reports support a role for Swi/Snf in repression of transcription, no experiments have tested whether Swi/Snf repression in vivo is direct or indirect, and if it involves the nucleosome-remodeling activity of Swi/Snf. Recent studies of two Swi/Snf-related complexes, Isw2 and RSC, have suggested that these complexes play direct roles in repression of transcription (Goldmark et al. 2000;Kent et al. 2001;Damelin et al. 2002;Ng et al. 2002).The experiments presented in this paper investigate the repression of the S. cerevisiae SER3 gene by Swi/Snf. Our results strongly suggest a direct role for Swi/Snf in transcriptional repression via controlling chromatin structure. Surprisingly, and in contrast to Swi/Snf activation, Swi/Snf repression has a strong requirement for only one Swi/Snf component, the Snf2 ATPase. Results and Discussion Repression of SER3 is dependent primarily on the Snf2 ATPaseTo investigate the role of Swi/Snf in transcriptional repression, we chose to study the S. cerevisiae SER3 gene, which encodes an enzyme required for serine...