Project description:The cooperation of transcriptional and post-transcriptional controls to shape gene regulation is poorly understood. Here we show that a combination of two simple and non-invasive genomic techniques, coupled with kinetic mathematical modelling, afford insight into the multi-layered regulation of gene expression dynamics in response to oxidative stress in the fission yeast Schizosaccharomyces pombe. This study reveals a dominant role of transcriptional control in response to stress, and it points to the first minutes after stress induction as a critical time when control of mRNA turnover can support transcriptional control for rapid gene regulation. In addition, we uncover specialized gene expression strategies such as simultaneous transcriptional repression and mRNA destabilization for genes encoding ribosomal proteins, delayed mRNA destabilization with varying contribution of transcription for the ribosome biogenesis regulon, dominant roles of mRNA stabilisation for genes participating in protein degradation, and adjustment of mRNA turnover during stress adaptation. We also show that genes regulated independently of the Atf1p transcription factor are mainly controlled by mRNA turnover during oxidative stress.
Project description:Gene expression is controlled globally and at multiple levels in response to environmental stress, but the relationships among these dynamic regulatory changes are not clear. Here we analyzed genome regulation in response to stress in the fission yeast, Schizosaccharomyces pombe, combining dynamic genome-wide data on mRNA levels and translational profiles with data on the levels of 2148 proteins (43% of proteome).
Project description:Cross-species hybridizations of Sordaria macrospora targets on Neurospora crassa microarrays were performed with targets derived from the S. macrospora wild type undergoing sexual development (wt.sex) and the mutant strains dSmtA-1 and dSmtA-2. For each strain, two independent experiments were carried out with a dye switch in the second experiment.<br><br>The following slide/target/dye combinations were done:<br><br>slide N16-86: Cy3-target: wt.sex (1), Cy5-target: dSmtA-1 (1)<br><br>slide N16-87: Cy3-target: dSmtA-1 (2), Cy5-target: dSmtA-2(2)<br><br>slide N16-88: Cy3-target: dSmtA-2 (1), Cy5-target: wt.sex (2)
Project description:Although much is known about the regulation of eukaryotic transcription, the global controls which determine rates of total transcription within a cell are not well understood. We have investigated the effects that the DNA to protein ratio has on both total cellular transcription and the transcription of individual mRNA genes in the unicellular eukaryote fission yeast. Mutants altered in cell size and those blocked in cell cycle progression were used to vary the DNA to protein ratio over a fivefold range around the wild type value. We find that cells of sizes within twofold of wild type value regulate global transcription to maintain similar transcription rates per protein regardless of the cellular DNA content. These changes in total transcription were correlated with coordinated changes in gene occupancy by RNA polymerase II. In large cell cycle arrested mutants, when the DNA to protein ratio falls to a low level, total transcription rates plateau as DNA becomes limiting for transcription1. Unexpectedly, expression levels of individual genes remained tightly coordinated with each other over the entire range of cell sizes. We propose that there is a coordinated, global cellular control which determines the rate of transcription of most genes in the genome and that this control plays a role in regulating the overall growth rate of the cell. Normalized data generated using protocol P-TABM-1335 is available in file ZHURINSKY_NORMALISED_DATA.txt in the additional data archive.
Project description:The relative amount of RNA polymerase II (Pol II) associated with a given ORF provides an estimate for transcriptional efficiency. We therefore established a systematic approach to measure Pol II occupancy using chromatin immunoprecipitation followed by analysis on microarrays