Figure 6

Hypothetical models explaining the potential biological significance of the cis-regulatory patterns revealed by phylogenetic footprinting. (A) Simplistic model of a hypothetical promoter from a stress-regulated bZIP transcription factor. Each colored box (tfbs1, tfbs2, etc.) represents a putative TFBS class recognized by specific cognate DNA-binding proteins (TF1, TF2, etc.). The boxes corresponding to tfbs-x, tfbs-y, and tfbs-z represent elements that are conserved between stress-associated orthologs and non-stress-associated paralogs. The spatially conserved ‘core module’ (boxed) is found in all orthologs but not in paralogs and is likely to define the basal regulatory program of the gene. The other tfbs classes outside the ‘core module’ represent the ‘regulatory fine-tuners’ that tend to exhibit lineage or species specificity. The tfbs classes marked with an asterisk represent the ‘regulatory fine-tuner’ that is likely specific and/or critical for a given stress signal. The model postulates that distinct signals act on a combination of tfbs, thus responses are configured by synergistic interaction of several TFs. The tfbs-TF combinations overlap between different stress and developmental signals facilitating an integrated response and distinct spatio-temporal pattern for each member of an orthologous group. (B) Simplistic model showing the divergence of cis-regulatory information content among orthologs and paralogs. The spatially conserved ‘core module’ (boxed) is conserved among the orthologs from monocot species (M1 and M2) as well as in the ortholog from the dicot species (D). The ‘core module’ diverged between orthologs and paralogs. In addition, both monocot (M) and dicot (D) paralogs have acquired other elements, represented by numbered white circles.