Fig. 3. PRE/TRE motifs and flexibility of PRE/TRE design. (A) DNA motifs shown to be important for PRE/TRE function. The Grh (Grainy head) protein binds to several different PRE/TRE sites. The motif shown is that found in PRE/TREs by Blastyak et al. (Blastyak et al., 2006). The Dsp1 protein also has broad DNA-binding specificity (Brickman et al., 1999). The motif shown is that used by Dejardin et al. (Dejardin et al., 2005). Gaf binds the same target sequence as Pipsqueak (Psq), suggesting that the two proteins may compete or cooperate at closely spaced sites. (B) Many of these motifs are important for regulating genes that do not have PRE/TREs, for example the Drosophila white gene which is regulated by the Zeste protein (600 bp of upstream regulatory region are shown). These motifs are also short and occur randomly in DNA, such as in the bacterial LacZ gene (the first 600 bp of the coding sequence are shown). (C) PRE/TREs have different combinations of motifs, with no preferred order or number. Shown here are 600 bp of the bxd and Fab-7 PREs from the Drosophila Bithorax complex, and of PRE/TREs from the Drosophila engrailed (en), vestigial (vg) and homothorax (hth) loci. Grey boxes show minimal PRE/TREs where these have been defined (Dejardin et al., 2005; Brown et al., 2005). Flanking sequences contain additional motif clusters which may contribute to the function of these PRE/TREs in their endogenous context.