Cracking the Code of Transcriptional Logic: Optimization of ETS Sites in Human Disease

Abstract

Recent experimental work has shown the importance of suboptimized transcription factor (TF) binding sites in synthetic enhancers for recapitulating a natural expression pattern within the neural plate of the ascidian Ciona. In particular, the suboptimization of binding sites of the ETS family of TFs was demonstrated to be crucial to tissue-specific expression. The ETS family of transcription factors binds a DNA core motif of 5’-GGA(A/T)-3’. The nucleotides flanking this core motif are variable, but deviation from the optimal flanking nucleotides lowers binding affinity of ETS to the sequence, thus suboptimizing the site. It has been suggested that suboptimized TF binding sites are also an important feature of native transcriptional regulatory elements that direct spatially and temporally specific transcription. This work probes the importance of the suboptimization of the flanking nucleotides of ETS binding sites by examining previously catalogued mutations within regulatory regions which cause human disease. Mutations causing polydactyly and corneal dystrophy alter the flanking nucleotides of predicted ETS sites to create higher affinity binding sites within regulatory DNA, resulting in ectopic expression of gene targets. This work therefore demonstrates the importance of suboptimized ETS sites in humans and suggests that they may be especially crucial in regulatory sequences with high densities of ETS sites.