The transcriptional regulation of entry and exit from stationary phase in S. cerevisiae

Marijana Radonjic, Jean-Christophe Andrau, Patrick P.C.W. Kemmeren, Philip Lijnzaad, Dik van Leenen, Frank C.P. Holstege. Genomics Laboratory, UMC Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands.

We are studying S.cerevisiae stationary phase (SP) as a model for quiescence. Initial goals are to determine SP-specific genes and investigate how the transcriptional program of SP is regulated. A 34 time-point microarray experiment covering SP exit, mid-log, diauxic shift and entry into SP was performed. To determine mRNA changes per cell, an external normalisation approach was applied. This reveals dramatic changes in the mRNA population across the time series, with rapid induction of genes upon SP exit and rapid decay prior to diauxic shift. This is followed by partial recovery and a slow decay phase upon SP entry. Despite the global mRNA downregulation in SP, 460 genes are induced in SP relative to the other genes. Most of these are already induced during diauxic shift, with only a fraction showing solely SP-specific induction. Phenotype analysis of 16 genes whose mRNA levels change in agreement with a putative role in SP, confirmed their requirement for SP. The rapid induction of genes upon SP exit indicates that the transcription machinery is maintained throughout SP, poised for rapid growth. To investigate this further, genome-wide location analysis (ChIP on chip) for RNA polymerase II was carried out, revealing dramatic re-localisation during exit and entry from SP as well as evidence for transcription during SP. The microarray data and follow up experiments provide a framework for further investigating how entry and exit from SP is regulated through transcription.

Program Nr. 379A from 2004 Yeast meeting

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