Microarray Analysis of the S. pombe Cell Cycle - Oliva et al, PLoS Biology 07/2005

Anna Oliva, Adam Rosebrock, Francisco Ferrezuelo, Saumyadipta Pyne, Haiying Chen, Steve Skiena, Bruce Futcher, and Janet Leatherwood

Stony Brook University, Stony Brook New York, 11794

PLoS Biology, July, 2005. PMID 15966770.


Microarrays were used to measure gene expression through the cell cycle of S. 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 genes were often involved in ribosome biogenesis, possibly explaining the cell cycle oscillation in protein synthesis in S. pombe. The G2/M wave of genes 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 regulated 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: 2000 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.

Figures included with the text:

For purple/yellow versions of the figures, click on the corresponding

(Click on linked image for a higher-resolution version)

• Figure 1: Cell Cycle Synchrony. Septation indexes for two elutriation and one cdc25-22 block release time course
• Figure 2: Distribution of p-values for cell-cycle regulated genes
• Figure 3: Cell cycle regulated genes ordered by time of peak expression
• Figure 4: Venn diagram of overlap between studies
• Figure 5: Overlap between different cell cycle microarray studies, by rank
• Figure 6: The number of genes peaking during each portion of the cell cycle
• Figure 7: Cluster analysis of the top 750 cellcycle regulated genes ()
• Figure 8: M-phase clusters, expanded view ()
• Figure 9: S/early G2 phase clusters, expanded view ()
• Figure 10: Mid to Late G2 phase clusters, expanded view ()
• Figure 11: Ribosome biognesis associated genes cycle in S. cerevisiae ()
• Figure 12: Distribution of Promoter Motifs

Supplementary Data Sets:

• Supplemental Figure S1: cdc18 expression, expanded view.
• Supplemental Table S1: Cell cycle annotated data.
• Supplemental Table S2: SpikeChart weight matricies.
• Supplemental Table S3: S. cerevisiae homologs of S. pombe cell cycle genes.
• Supplemental Data S1: Data files for interactive visualization in JavaTreeView.

Normalized Data Sets:

• Timecourse following "elutriation A" synchronization, 3 cell cycles. 50 hybridizations:
  Download data (Tab Delimited Text)
• Timecourse following "elutriation B" synchronization, 3 cell cycles. 41 hybridizations [E-TABM-5]:
  Download data (Tab Delimited Text)
• Timecourse following cdc25-22 block-release synchronization, 3 cell cycles. 52 hybridizations [E-TABM-8]:
  Download data (Tab Delimited Text)
• Various additional hybridizations, including cdc10-m22, low nitrogen growth. 27 hybridizations:
  Download data (Tab Delimited Text)



Complete data for all pombe cell-cycle experiments, Rustici et al, Peng et al, Oliva et al can be downloaded here.

last modified Tuesday, 28-Jun-2005 06:05:02 GMT	RedGreenGene.com data curator feedback