Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

Abstract

We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures synchronized by three independent methods: alpha factor arrest, elutriation, and arrest of a cdc15 temperature-sensitive mutant. Using periodicity and correlation algorithms, we identified 800 genes that meet an objective minimum criterion for cell cycle regulation. In separate experiments, designed to examine the effects of inducing either the G1 cyclin Cln3p or the B-type cyclin Clb2p, we found that the mRNA levels of more than half of these 800 genes respond to one or both of these cyclins. Furthermore, we analyzed our set of cell cycle-regulated genes for known and new promoter elements and show that several known elements (or variations thereof) contain information predictive of cell cycle regulation. A full description and complete data sets are available at http://cellcycle-www.stanford.edu

Figure 1

Gene expression during the yeast cell cycle. Genes correspond to the rows, and the time points of each experiment are the columns. The ratio of induction/repression is shown for each gene such that the magnitude is indicated by the intensity of the colors displayed. If the color is black, then the ratio of control to experimental cDNA is equal to 1, whereas the brightest colors (red and green) represent a ratio of 2.8:1. Ratios >2.8 are displayed as the brightest color. In all cases red indicates an increase in mRNA abundance, whereas green indicates a decrease in abundance. Gray areas (when visible) indicate absent data or data of low quality. Color bars on the right indicate the phase group to which a gene belongs (M/G1, yellow; G1, green; S, purple; G2, red; M, orange). These same colors indicate cell cycle phase along the top. (A) Gene expression patterns for cell cycle–regulated genes. The 800 genes are ordered by the times at which they reach peak expression. (B) Genes that share similar expression profiles are grouped by a clustering algorithm as described in the text. The dendrogram on the left shows the structure of the cluster.

Figure 1

Gene expression during the yeast cell cycle. Genes correspond to the rows, and the time points of each experiment are the columns. The ratio of induction/repression is shown for each gene such that the magnitude is indicated by the intensity of the colors displayed. If the color is black, then the ratio of control to experimental cDNA is equal to 1, whereas the brightest colors (red and green) represent a ratio of 2.8:1. Ratios >2.8 are displayed as the brightest color. In all cases red indicates an increase in mRNA abundance, whereas green indicates a decrease in abundance. Gray areas (when visible) indicate absent data or data of low quality. Color bars on the right indicate the phase group to which a gene belongs (M/G1, yellow; G1, green; S, purple; G2, red; M, orange). These same colors indicate cell cycle phase along the top. (A) Gene expression patterns for cell cycle–regulated genes. The 800 genes are ordered by the times at which they reach peak expression. (B) Genes that share similar expression profiles are grouped by a clustering algorithm as described in the text. The dendrogram on the left shows the structure of the cluster.

Figure 2

Binding site frequencies. The distribution of various promoter elements in the upstream regions of each the five cell cycle–regulated groups and a control group of 279 non-cell cycle–regulated genes that do not respond to either Cln3p or Clb2p induction are graphically displayed. In each case the numbers on the x axes represent distance from the start codon, and the bars represent the frequency of a particular site per residue per gene at that position in the upstream promoter regions. N is any base; Y is C or T; W is A or T; R is A or G; and M is A or C. (A) SCB. (B) A variant on the SCB, which is also similar to an MCB. (C) MCB. (D) MCB_d, a degenerate MCB sequence. (E) MCM1/SFF site. (F) Swi5e, an extended Swi5 site.

Figure 3

The G1 clusters. The transcription profiles are displayed as described in the legend to Figure 1. (A) CLN2 cluster. A fraction of the genes regulated similarly to the G1 cyclin CLN2, which reaches peak expression in the G1 phase of the cell cycle. To view the full cluster of all the cell cycle–regulated genes, visit http://cellcycle-www.stanford.edu. (B) Y′ cluster. Thirty-one genes that are located within the Y′ elements show cell cycle regulation of mRNA levels that peak in G1.

Figure 4

The S and M clusters. The transcription profiles are displayed as described in the legend to Figure 1. (A) Histone cluster. The eight genes encoding histones and the yeast histone H1 homologue cluster very tightly and are expressed during S phase of the yeast cell cycle. (B) MET cluster. The expression of many of the members of the methionine pathway peaks just after the histones. (C) CLB2 cluster. A subcluster of genes that are expressed similarly to CLB2 highlights genes that peak during M phase.

Figure 5

The MCM1 + SFF consensus. By aligning promoter elements of several coregulated genes found in the CLB2 cluster (see our web site for the alignment), we developed a matrix for a new MCM1 + SFF consensus. The number of times each base was found at each position in the site was tallied and is displayed. The consensus was determined by examining the nucleotide frequencies at each position.

Figure 6

The M/G1 clusters. The transcription profiles are displayed as described in the legend to Figure 1. (A) MCM cluster. The MCM genes are involved in initiation of DNA replication and are coregulated during the M/G1 transition of the cell cycle. (B) SIC1 cluster. Twenty-seven genes that peak at the M/G1 boundary form a subcluster. (C) MAT cluster. This is a cluster of 13 coregulated genes expressed at the M/G1 boundary, many of which are involved in mating.

Figure 7

Cell cycle–regulated genes with characterized functions. Two hundred ninety-seven of the cell cycle–regulated genes are grouped by both function and phase of peak expression. Several functional groups are split into subgroups, which reflect the nature of the function. Those highlighted in red were previously known to be cell cycle regulated. Many functional categories display strong biases toward gene expression during particular intervals of the cell cycle. Obvious examples include genes involved in DNA synthesis and DNA repair (G1), mating (M, M/G1, and G1), chromatin structure (G1 and S), and methionine biosynthesis (S and G2).

Figure 8

Tubulin message levels. The mRNA levels for TUB1, TUB2, and TUB3, relative to those of PPA1, were determined during synchronous division after release from an α factor arrest, using the TAQman assay as described in MATERIALS AND METHODS.

Figure 9

Aggregate CDC score is largely independent of the cdc28 data set. Scatter plot for the scores that were derived using either the cdc15 and α factor experiments only (plotted on the y axis) or using the cdc15, the α factor, and the cdc28 experiments (x axis). A single dot is plotted for each gene. It should be noted that adding data increases the absolute magnitude of the scores; it is the relative magnitude, however, that indicates cell cycle regulation.