Fig. 5. Consequences of enhancer-transcription factor co-evolution. (A,B) Sets of orthologous transcription factors control expression of an orthologous target in species A (blue) and B (red). Note that although the order of individual binding sites is rearranged, in both cases transcription factors are co-adapted, as reflected by their different shapes, to form a complex and result in strong activation of expression. (C) If transcription factor 1 in species A is replaced by its ortholog from species B, it could bind to the target previously occupied by its ortholog. It could also interact although less well (as indicated with a broken line) with other transcription factors bound to the enhancer, resulting in weaker transcriptional activation. (D) If an entire enhancer is placed into a heterospecific context, individual transcription factors may be able to bind to their respective target sequences. Their interactions, however, are likely to be greatly hampered, thus resulting in no transcriptional activation or in activation in a different pattern because of serendipitous occurrence of binding sites recognized in other tissues.