Figure 1

Mechanisms for generating transcription factor diversity and limiting novel function to specific contexts. Many of these mechanisms are modular and may be mixed and matched to offer even greater evolutionary flexibility. A. Gene duplication, exon shuffling, and modular DNA binding allow transcription factors to increase and change their functionality. While gene duplicates are frequently lost, retention of both copies relaxes constraint and allows the paralogs to diverge through acquisition of mutations (indicated by purple ancestral copy splitting into red and blue versions). Exon shuffling allows transcription factors to evolve new function through acquisition of domains, shown here as a red exon swapped for blue exon. DNA binding can evolve in modular ways too. Here, the red homolog recognizes the red binding site, but the purple homolog can bind both red and blue binding sites. Specificity for the blue site could change without altering functions governed by the red site. B. Alternative splicing, protein-protein interactions, and post-translational modifications also increase transcription factor diversity, but these mechanisms also offer context specificity. Alternate splicing can lead to tissues that differ in the version of a transcription factor. Here, the version with the purple exon may have different functional abilities than the all blue version. Protein-protein interactions are particularly important to transcription factor function, since this ability determines whether the protein can successfully alter chromatin or recruit RNA polymerase. However, both interaction partners must be present to exert function, which means that these interactions can be controlled by limiting expression domain (C). Likewise, post-translational modifications are important for altering transcription factor modularity, and are context specific owing to the requirement of co-expression with a modifying enzyme. C. cis-regulatory module (CRM) level control of gene expression, restricts splice variants, interaction partners, and modifying proteins to distinct spatiotemporal contexts.