Identification of Cell Cycle-regulated Genes in Fission Yeast

Abstract

Cell cycle progression is both regulated and accompanied by periodic changes in the expression levels of a large number of genes. To investigate cell cycle-regulated transcriptional programs in the fission yeast Schizosaccharomyces pombe, we developed a whole-genome oligonucleotide-based DNA microarray. Microarray analysis of both wild-type and cdc25 mutant cell cultures was performed to identify transcripts whose levels oscillated during the cell cycle. Using an unsupervised algorithm, we identified 747 genes that met the criteria for cell cycle-regulated expression. Peaks of gene expression were found to be distributed throughout the entire cell cycle. Furthermore, we found that four promoter motifs exhibited strong association with cell cycle phase-specific expression. Examination of the regulation of MCB motifcontaining genes through the perturbation of DNA synthesis control/MCB-binding factor (DSC/MBF)-mediated transcription in arrested synchronous cdc10 mutant cell cultures revealed a subset of functional targets of the DSC/MBF transcription factor complex, as well as certain gene promoter requirements. Finally, we compared our data with those for the budding yeast Saccharomyces cerevisiae and found ϳ140 genes that are cell cycle regulated in both yeasts, suggesting that these genes may play an evolutionarily conserved role in regulation of cell cycle-specific processes. Our complete data sets are available at http://giscompute.gis.a-star.edu.sg/ϳgisljh/CDC.

Role of the RNA-binding Protein Nrd1 and Pmk1 Mitogen-activated Protein Kinase in the Regulation of Myosin mRNA Stability in Fission Yeast

“…As shown in Figure 9C, the Cdc4 mRNA levels also oscillate with a peak around the M phase to G1 phases, reaching a minimum around the G2 phase (180 min). These results are in agreement with those of genome-wide studies on cell cycle-dependent gene expression in fission yeast (Rustici et al, 2004;Peng et al, 2005). Notably, a decrease in the Cdc4 expression levels coincided with an increase in Nrd1 phosphorylation, further supporting our hypothesis that Nrd1 binds to and stabilizes Cdc4 mRNA and that Nrd1 RNA-binding activity is negatively regulated by its phosphorylation.…”

A Conserved SET Domain Methyltransferase, Set11, Modifies Ribosomal Protein Rpl12 in Fission Yeast

“…3C). Taken together, these results suggest that Rpl12 is a physiological substrate of Set11 and that the Lys 3 , and potentially Lys 39 and Lys 40 , of Rpl12 are the candidate target residues for Set11 activity.…”

“…By analyzing the MS/MS results, we were also able to identify a monomethylation at Arg 66 (supplemental Fig. S1C) and a methylation and/or another modification(s) at Lys 39 and Lys 40 ( Table 2). The most frequently observed mass for the latter region was a dimethylation at Lys 39 (supplemental Table S2).…”

Cell cycle progression in Escherichia coli B/r affects transcription of certain genes: Implications for synthetic genome design

“…Cell cycle-related fluctuations were detected for 2%, 5%, and 3-13% of the transcripts in human primary fibroblasts (Cho et al, 2001), HeLa cells (Whitfield et al, 2002) and yeast cells (Cho et al, 1998;Oliva et al, 2005;Peng et al, 2005;Rustici et al, 2004;Spellman et al, 1998), respectively. Despite the range of organisms studied, one characteristic common to these gene sets was that functionally related genes were co-transcribed.…”