Defining the molecular basis of the gene regulatory code

In the same way that the mRNA-binding specificities of transfer-RNAs define the genetic code, the DNA-binding specificities of transcription factors (TFs) form the molecular basis of the gene regulatory code. The gene regulatory code is far more complex than the genetic code, in particular because there are more than 1600 TFs that commonly interact with each other. TF-TF interactions are required for cell fate specification and execution of cell-type specific transcriptional programs. Despite this, the interaction landscape between DNA-bound transcription factors is poorly defined. Here, we have mapped the biochemical interactions between DNA-bound TFs using CAP-SELEX, a method that can simultaneously identify individual TF binding preferences, TF-TF interactions and the DNA sequences that are bound by the interacting complexes. A screen of more than 60,000 TF-TF pairs identified 2207 novel interactions, including 1807 spacing preferences and 400 composite motifs. We estimate that the screen discovered ~ 25% of human TF-TF motifs. The novel composite motifs we discovered were enriched in cell-type specific elements, active in vivo and more likely to be formed between developmentally co-expressed TFs. Furthermore, TFs that define embryonic axes commonly interacted with different TFs and bound to distinct motifs, explaining how TFs with similar specificity can define distinct cell types along developmental axes.