Periodic gene expression program of the fission yeast cell cycle

Abstract

Cell-cycle control of transcription seems to be universal, but little is known about its global conservation and biological significance. We report on the genome-wide transcriptional program of the Schizosaccharomyces pombe cell cycle, identifying 407 periodically expressed genes of which 136 show high-amplitude changes. These genes cluster in four major waves of expression. The forkhead protein Sep1p regulates mitotic genes in the first cluster, including Ace2p, which activates transcription in the second cluster during the M-G1 transition and cytokinesis. Other genes in the second cluster, which are required for G1-S progression, are regulated by the MBF complex independently of Sep1p and Ace2p. The third cluster coincides with S phase and a fourth cluster contains genes weakly regulated during G2 phase. Despite conserved cell-cycle transcription factors, differences in regulatory circuits between fission and budding yeasts are evident, revealing evolutionary plasticity of transcriptional control. Periodic transcription of most genes is not conserved between the two yeasts, except for a core set of approximately 40 genes that seem to be universally regulated during the eukaryotic cell cycle and may have key roles in cell-cycle progression.

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.…”

Rearrangements of the transcriptional regulatory networks of metabolic pathways in fungi

“…Early evidence for changes in gene regulation among fungi came from transcriptional profiling studies comparing S. cerevisiae, S. pombe and C. albicans [13][14][15]. Furthermore, predictions of cis-regulatory sequences, and meta-analyses of gene co-expression revealed that transcription networks have a great deal of flexibility [4,[16][17][18].…”

A Systematic Screen for Transcriptional Regulators of the Yeast Cell Cycle

“…Cell cycle transcription was initially believed to be important but limited (Price et al 1991) until genomewide expression profiling and chromatin immunoprecipitation (ChIP-chip) experiments revealed that cell cycle transcription is remarkably complex, involving a growing number of transcription factors and a large number of periodically transcribed genes in organisms from bacteria to yeast, plants, and animals (Cho et al 1998;Spellman et al 1998;Laub et al 2000;Whitfield et al 2002;Menges et al 2003;Rustici et al 2004). In the yeast Saccharomyces cerevisiae, cell cycle transcription involves at least 800 periodically transcribed genes ($14% of the genome) (Spellman et al 1998;Pramila et al 2006) and to date more than a dozen transcription factors involved in numerous regulatory complexes and feedback loops (reviewed in Breeden 2003 andReed 2005).…”