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Poised for Action

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Science's STKE  19 Apr 2005:
Vol. 2005, Issue 280, pp. tw147
DOI: 10.1126/stke.2802005tw147

The current model for gene expression in response to environmental change involves recruitment of transcription factors and RNA polymerase II (RNA Pol II) to the DNA. Radonjic et al. challenge this view with evidence that, in stationary-phase yeast, RNA Pol II is already bound to intergenic DNA upstream of genes that will be rapidly stimulated in yeast following exit from the quiescent state. Changes in poly(A) mRNA were quantified after stationary cells were introduced into glucose-rich medium, and three peaks in mRNA abundance were detected during the progression back to stationary phase (a 9-day process), as well as a sharp rise in mRNA abundance between 15 and 25 minutes after glucose repletion. Microarray analysis indicated that 769 genes were stimulated between 2- and 35-fold within 6 minutes of exit from stationary phase. There was also a set of genes that were induced just prior to entry of stationary phase and that remained enriched in stationary-phase cells for several days, suggesting active transcription in stationary cells. The abundance of several components of the transcriptional machinery was similar in stationary- and mid-log-phase cells, although the phosphorylation of the C-terminal domain (CTD) of the largest subunit of RNA Pol II was less in stationary-phase cells. Using genome-wide chromatin immunoprecipitation (ChIP on a chip), RNA Pol II was enriched on more than 1300 DNA sites in stationary cells and on ~3200 sites on mid-log-phase cells. One difference was the frequency with which RNA Pol II was found on intergenic regions (higher in stationary-phase cells relative to mid-log-phase cells) and gene-coding regions (higher in mid-log-phase cells). More detailed analysis of the DNA containing a gene that is enriched in stationary phase showed that RNA Pol II was bound along the gene-encoding region for PUT4, consistent with active transcription. Detailed analysis of a gene that is immediately up-regulated upon exit from stationary phase, SUT1, showed that RNA Pol II was bound in the intergenic region. The authors emphasize two results from their work. First, transcription is not completely shut down in stationary-phase cells, and they may be capable of responding to environmental changes without leaving stationary phase through the limited active RNA Pol II present. Second, RNA Pol II binding to DNA may not be the rate-limiting step in transcription for the genes that are rapidly stimulated following exit from stationary phase; instead, RNA Pol II may be bound in the intergenic region but the activity may be repressed by the state of phosphorylation, allowing a rapid response at these genes.

M. Radonjic, J.-C. Andrau, P. Lijnzaad, P. Kemmeren, T. T. J. P. Kockelkorn, D. van Leenen, N. L. van Berkum, F. C. P. Holstege, Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol. Cell 18, 171-183 (2005).[Online Journal]

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