Figure 3.

Multimodality of the Reb1 transcription factor. A part of the selection network containing motifs that are associated with Reb1 is shown in greater detail. All nodes represent variants of the Reb1 consensus. Note that in this figure, all selection network arcs, including those with low confidence, are plotted, and reverse complement motifs are not combined. (A) Reb1 motifs. (B) Reb1 reverse complementing motifs. Black arcs represent high substitution rate (low selective pressure). Blue arcs represent low substitution rate (high selective pressure). A clear two-family structure emerges, where low-rate arcs are separating a large Reb1 family from a smaller one. The structure is mirrored in the reverse complement motifs. The Reb1 promoter (C) contains two autoregulatory sites, each located in a different family, with distinct binding site affinities (Ideker et al. 2001). This raises the hypothesis of two distinct Reb1 modes of operation, each activating a different group of motifs in specific concentration. Note that nodes in the network are octamers and that the Reb1 consensus is a septamer.