Fig. 5. Simulation of the network illustrated in Fig. 1 using various levels of N. The initial state of Ume6/Rpd3 was 9, and the rest were 0. Filled squares, IME1 RNA; open squares, Ime1; filled triangles, IME2 RNA; open triangles, Ime2

Fig. 6. Types of trajectories observed under abnormal conditions.

Fig. 7. Self-degradation of Ime1 and Ime2 are required for the transient transcription of their genes. (A and B) Simulation of the network upon deletion of either the Ime1 self-degradation loop (A) or the Ime2 self-degradation loop (B). The latter resulted in two types of trajectories. The initial state of Ume6/Rpd3 was 9, and the rest were 0. Filled square, IME1 RNA; open squares, Ime1; filled triangles, IME2 RNA; open triangles, Ime2

Fig. 8. Simulation of the network when X's state was 1 in the initial vectors. Karnaugh-like maps show the functional dependence between initial states and the type of behavior of the trajectory. Each cell in the table represents a specific initial vector. The rows of the tables are indexed by the initial states of IME1 RNA and proteins, respectively, and the columns are indexed by the similar states of IME2. The numbers in the cells indicate the length of the trajectory of the corresponding initial vector. The cells are marked by different colors representing the following four types of trajectories' behavior (see SI Fig. 6): normal transient expression (green); restrained expression with weak transience (yellow); short trajectories, expression not induced (purple); and IME1 expression is weak but transient, whereas IME2 is not expressed or expressed before Ime1 (turquoise).

Fig. 9. The role of Ime1 and Ime2 in the negative feedback regulation. Experimental results validate the computational model. (A and B) Simulation of the network upon deletion of all edges coming out of IME1 (A) or IME2 (B). The initial state of Ume6/Rpd3 was 9, and the rest were 0. Filled squares, IME1 RNA; open squares, Ime1; filled triangles, IME2 RNA; open triangles, Ime2. (C) Experimental results. Isogenic diploid cells deleted for either IME1 (filled circles) or IME2 (open circles) (strains Y424 and Y443, respectively) that carried the ime1-lacZ reporter (pAS128) as described in ref. 1. Cells were shifted to meiotic conditions, and at the indicated hours, RNA was extracted and its level checked by quantitative PCR. The level of IME1 mRNA was measured either directly (in the ime2D strain) or indirectly by checking the level of lacZ RNA (in the ime1D strain).

1. Shefer-Vaida M, Sherman A, Ashkenazi T, Robzyk K, Kassir Y (1995) Dev Genet 16:219-228.