Comparison of expression patterns of key cell cycle-regulated genes in slowly growing [YMC (14), Left] vs. rapidly growing [cdc15, alpha, and cdc28 (1, 5)] yeast cultures. (Upper) G₂ cyclin CLB1, mitotic transcription factor SWI5, and G₁ cyclin CLN3. (Lower) Mitotic cyclin PCL9 and MCM subunit MCM3. Environment-dependent G₁ phase is ≈10 times longer in YMC than found in previous studies (cdc15, alpha, and cdc28 synchronization), allowing the expression of key cell cycle genes to be timed with higher accuracy.

Transcriptional program of the yeast cell cycle. (A and B) Proteins involved in DNA replication initiation, color-coded according to timing of their expression. The prereplication complex (pre-RC) undergoes several changes before an elongation complex (EC), capable of initiating DNA synthesis, is formed (24). The order of expression (A) agrees with the order in which gene products are needed (B). In A, dotted outlines denote non-CCTR genes. Note the two groups of MCM subunits, each containing one nuclear localization signal (NLS). In B, solid outlines denote primary expression peak; dashed outlines denote secondary (lower scoring) peak. The only exception to just-in-time transcription is ORC1. (C) Timing of CCTR complexes. DSE, daughter-cell-specific expression program; APC act, APC activation; SPB sat, spindle pole body satellite formation; SPB sep, spindle pole body duplication and separation. (D) Peaks of selected CCTR genes. (E) Phases and subphases of the cell cycle. Note new prereplicative G₁ (P) phase. (F) Histogram of expression peaks of CCTR genes. (G) Peaks of transcripts regulated by selected cell cycle transcription factors (11, 20, 21, 29, 30). Note the differences in expression of MBF and SBF targets. (H) Histograms of peaks of CCTR genes involved in selected cell cycle functions. Compare peaks of predicted Cdc28p targets (26) vs. peaks of CDC28 (D).

Characteristic temporal profile of cell cycle-regulated genes. Presented are the raw expression data (14) of several transcripts that peak at different times: cyclins (CLN3, CLN2, CLB1, and PCL9); a Cdc28p inhibitor (SWE1); a positive regulator of mitotic exit (SPO12); and an endochitinase, crucial for cell separation after mitosis (CTS1). y axis, normalized expression (arbitrary units); x axis, time in minutes.

Expression profiles measured for the whole culture differ considerably from single-cell mRNA profiles. Imperfect synchronization of cells results in broadening of expression profiles measured in the culture (Right), compared with the respective single-cell profiles (Left). The original single-cell expression profiles (A, C, and E) can be reconstructed from the observed profiles (B, D, and F, respectively) by using deconvolution. This method can also be applied when the single-cell expression profile is complex (C and E) rather than just one short-lived pulse (A).