title: Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit.
abstract: The resting state of eukaryotic cells (G0) is relatively uncharacterized. We have applied DNA microarray expression profiling of S. cerevisiae to reveal multiple transitions during a complete 9-day growth cycle between stationary phase (SP) exit and entry. The findings include distinct waves of transcription after the diauxic shift (DS), identification of genes active in SP, and upregulation of over 2500 genes during the first minutes of lag phase. This provides a framework for analyzing large-scale reprogramming of gene expression. Despite global repression, the general transcription machinery is found to be present in quiescent cells but is largely inactive. Genome-wide location analysis by chromatin immunoprecipitation (ChIP on chip) reveals that RNA polymerase II is more predominantly bound at intergenic regions in SP, upstream of hundreds of genes immediately induced upon exit. In contrast to current models of activation-coupled recruitment, the results show that RNA polymerase II is located and maintained upstream of many inactive genes in quiescence.
authors.affiliation: Department of Physiological Chemistry, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.
authors.forename: Marijana
authors.initials: M
authors.lastname: Radonjic
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Andrau
authors.forename: Philip
authors.initials: P
authors.lastname: Lijnzaad
authors.forename: Patrick
authors.initials: P
authors.lastname: Kemmeren
authors.forename: Thessa T J P
authors.initials: TT
authors.lastname: Kockelkorn
authors.forename: Dik
authors.initials: D
authors.lastname: van Leenen
authors.forename: Nynke L
authors.initials: NL
authors.lastname: van Berkum
authors.forename: Frank C P
authors.initials: FC
authors.lastname: Holstege
mesh_terms: D047369:Chromatin Immunoprecipitation; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D015151:Immunoblotting; D020411:Oligonucleotide Array Sequence Analysis; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism*; D016196:S Phase; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics* / Q000254:growth & development; D014158:Transcription, Genetic
chemical_list: D012319:RNA Polymerase II