In a typical eukaryotic cell there is a significant difference in abundance between the rarest and most common mRNAs. This is largely due to differences in gene transcription which, in turn, are believed to be due to the combinations of the specific promoter-binding transcription factors interacting with the general transcription machinery of the cell. It now turns out that the general transcription machinery itself imposes a level of regulation on top of that due to gene-specific factors. Using high-density oligonucleotide arrays (or gene chips) to monitor genome-wide expression in Saccharomyces cerevisiae, Holstege et al.1 Holstege F.C.P. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998; 95: 717-728 Abstract Full Text Full Text PDF PubMed Scopus (1590) Google Scholar took advantage of yeast with temperature-sensitive or point mutations in the components of the transcriptional apparatus. They asked the question: what genes are affected by these mutations? What emerged was a complete surprise. While some mutations affect most genes, such as those in the core RNA polymerase, mutations in other components affect specific, but different subsets of genes. For instance, loss of Srb5p alters only 16% of genes, mainly those of the pheromone-response pathway and, indeed, further work showed srb5 mutants have a defect in mating efficiency. The factor Srb10p turns out to be a negative regulator of 173 genes, nearly half of which are derepressed in nutrient-starved cells. This type of approach complements work described by Spellman et al.2 Spellman P.T. et al. Comprehensive identification of cell-cycle-regulated genes of the yeast Sacchromyces cerevisiae by microarray hybridisation. Mol. Biol. Cell. 1998; 9: 3273-3297 Crossref PubMed Scopus (3867) Google Scholar , who used DNA microarrays and statistical techniques to identify 800 genes whose transcripts oscillate through one peak per cell cycle. Yeast cultures were synchronized by α-factor arrest, elutriation or arrest of a cdc15 temperature-sensitive mutant and cell-cycle-regulated genes were defined using a Fourier algorithm for periodicity and correlation algorithm for RNA levels. Periodicity of expression for half these genes can be accounted for mechanistically by the presence of SBF- and MBF-binding sites in many promoter elements. Expression of most genes also responds to induction of G1 cyclin, Cln3p and the B-type cyclin, Clb2p. Interestingly, Holstege et al.1 Holstege F.C.P. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998; 95: 717-728 Abstract Full Text Full Text PDF PubMed Scopus (1590) Google Scholar show that TAFII145 temparature-sensitive mutants arrest in G1–S and many genes showing transcriptional dependency on TAFII145 function in cell-cycle progression. Holstege et al.1 Holstege F.C.P. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998; 95: 717-728 Abstract Full Text Full Text PDF PubMed Scopus (1590) Google Scholar discuss the potential for determining which components of the general and gene-specific transcriptional machinery have essential roles at any particular promoter. By combining data from studies similar to those of Holstege et al.1 Holstege F.C.P. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998; 95: 717-728 Abstract Full Text Full Text PDF PubMed Scopus (1590) Google Scholar and Spellman et al.2 Spellman P.T. et al. Comprehensive identification of cell-cycle-regulated genes of the yeast Sacchromyces cerevisiae by microarray hybridisation. Mol. Biol. Cell. 1998; 9: 3273-3297 Crossref PubMed Scopus (3867) Google Scholar it might become possible to ‘map’ these levels of control for each stage of the cell cycle. Determining which genes are affected when part of the transcription machinery is mutated (a ‘bottom-up’ approach) and how the ‘transcriptome’ changes in different physiological states (a ‘top-down’ approach) should increase our understanding of what turns genes on and off.
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