Generic binding sites, generic DNA-binding domains: where does specific promoter recognition come from?

A transcription reaction relies on the specific recognition of cis-regulatory regions containing short DNA motifs. Such sequences are bound by transcription factors (TFs) involved in the recruitment, direct or not, of the transcriptional machinery. A eukaryotic genome can contain tens of genes encoding TFs that recognize very similar consensus DNA target sequences. In this review, we explore in a simple way how TFs coexpressed in the same cells and recognizing generic consensus sites with generic DNA-binding domains can achieve a specific modulation of target gene expression. We dissect the strategy followed by eukaryotes, which involves the formation of complex nucleoprotein structures involving many TFs and their cognate binding sites. This multiplicity of actors increases the effective length of the target DNA recognized by the TFs and might help paralogous TFs establish specific interactions. From this perspective, eukaryotic gene regulation implies the cooperation of several TFs, which is also the basis of information integration. Such cooperative TFs are likely to form a combinatorial partner code whose ultimate molecular hallmark is the assembly of enhanceosome-like structures ensuring the formation of an activation surface that is complementary to other coactivators and to the transcriptional machinery itself.