The Cell Cycle–Regulated Genes of Schizosaccharomyces pombe

Abstract

Many genes are regulated as an innate part of the eukaryotic cell cycle, and a complex transcriptional network helps enable the cyclic behavior of dividing cells. This transcriptional network has been studied in Saccharomyces cerevisiae (budding yeast) and elsewhere. To provide more perspective on these regulatory mechanisms, we have used microarrays to measure gene expression through the cell cycle of Schizosaccharomyces pombe (fission yeast). The 750 genes with the most significant oscillations were identified and analyzed. There were two broad waves of cell cycle transcription, one in early/mid G2 phase, and the other near the G2/M transition. The early/mid G2 wave included many genes involved in ribosome biogenesis, possibly explaining the cell cycle oscillation in protein synthesis in S. pombe. The G2/M wave included at least three distinctly regulated clusters of genes: one large cluster including mitosis, mitotic exit, and cell separation functions, one small cluster dedicated to DNA replication, and another small cluster dedicated to cytokinesis and division. S. pombe cell cycle genes have relatively long, complex promoters containing groups of multiple DNA sequence motifs, often of two, three, or more different kinds. Many of the genes, transcription factors, and regulatory mechanisms are conserved between S. pombe and S. cerevisiae. Finally, we found preliminary evidence for a nearly genome-wide oscillation in gene expression: 2,000 or more genes undergo slight oscillations in expression as a function of the cell cycle, although whether this is adaptive, or incidental to other events in the cell, such as chromatin condensation, we do not know.

Cdc7-Dbf4 RegulatesNDT80Transcription as Well as Reductional Segregation during Budding Yeast Meiosis

“…Total RNA was prepared from snap-frozen cells as directed (RiboPure-Yeast; Ambion, Austin, TX), and labeled cDNA was prepared as described previously (Oliva et al, 2005). Two-color hybridization of 10-h samples and their 0-h controls was performed on custom arrays of spotted long PCR probes.…”

Roles of the CDK Phosphorylation Sites of Yeast Cdc6 in Chromatin Binding and Rereplication

“…Labeled cDNA probe was synthesized from 4 g purified genomic DNA incubated with 240 M aminoallyl-dUTP (aadUTP), 200 ng/ l random hexamer, 360 M dNTPs, and 120 M dTTP using Klenow fragment at 37°C for 4 -5 h. The resulting aadUTP-cDNA probe was purified using the Qiagen PCR purification kit and coupled with Cy3 or Cy5 fluorescent dye using a protocol from TIGR (http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml). Purified coupled cDNAs corresponding to 100 pmol Cy3 and 100 pmol Cy5 were mixed together and hybridized, as described by Oliva et al (2005), to microarrays printed by spotting PCR products onto glass slides coated with amino-propylsilane. These microarrays were exactly as described (Oliva et al, 2005), but with S. cerevisiae PCR fragments.…”

“…Purified coupled cDNAs corresponding to 100 pmol Cy3 and 100 pmol Cy5 were mixed together and hybridized, as described by Oliva et al (2005), to microarrays printed by spotting PCR products onto glass slides coated with amino-propylsilane. These microarrays were exactly as described (Oliva et al, 2005), but with S. cerevisiae PCR fragments.…”

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.…”