Abstract
Transcription by RNA polymerase II in Saccharomyces cerevisiae and in humans is widespread, even in genomic regions that do not encode proteins1,2,3,4,5,6. The purpose of such intergenic transcription is largely unknown, although it can be regulatory7,8. 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 medium9. 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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Acknowledgements
We thank A. Dudley, A. Duina and J. Wu for comments on the manuscript. We also thank P. Cliften, P. Sudarsanam and M. Johnston for sharing unpublished results, and J. O'Sullivan and N. Proudfoot for advice on transcription run-on experiments. This work was supported by a grant from the National Institutes of Health to F.W. and by a postdoctoral fellowship from the Canadian Institute for Health Research to J.A.M.
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Supplementary information
Supplementary Table 1
List of S. cerevisiae strains used.
Supplementary Figure 1
Alignment of DNA sequence 5' of the SER3 gene of five related yeasts.
Supplementary Figure 2
Deletion analysis of the SER3 promoter region.
Supplementary Figure 3
Northern analysis of total and poly(A)-enriched RNA.
Supplementary Figure 4
Northern analysis of SRG1, SER3, and SNR190 (loading control) RNA levels in wild type and snf2Δ strains.
Supplementary Figure 5
Quantitation of the ChIP data shown in Figure 4.
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Martens, J., Laprade, L. & Winston, F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429, 571–574 (2004). https://doi.org/10.1038/nature02538
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DOI: https://doi.org/10.1038/nature02538
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