A regulatory role for repeated decoy transcription factor binding sites in target gene expression

摘要

AbstractTandem repeats of DNA that contain transcription factor (TF) binding sites could serve as decoys, competitively binding to TFs and affecting target gene expression. Using a synthetic system in budding yeast, we demonstrate that repeated decoy sites inhibit gene expression by sequestering a transcriptional activator and converting the graded dose–response of target promoters to a sharper, sigmoidal-like response. On the basis of both modeling and chromatin immunoprecipitation measurements, we attribute the altered response to TF binding decoy sites more tightly than promoter binding sites. Tight TF binding to arrays of contiguous repeated decoy sites only occurs when the arrays are mostly unoccupied. Finally, we show that the altered sigmoidal-like response can convert the graded response of a transcriptional positive-feedback loop to a bimodal response. Together, these results show how changing numbers of repeated TF binding sites lead to qualitative changes in behavior and raise new questions about the stability of TF/promoter binding.SynopsisRepetitive stretches of DNA that contain transcription factor (TF) binding sites can act as decoys that sequester TFs. This study shows that these decoy sites can have important indirect effects on transcriptional regulation by altering the dose–response between a TF and its target promoter.To probe the ability of TF decoy sites to alter gene expression, we used a synthetic genetic strategy in Saccharomyces cerevisiae based on the tet–OFF system.We show that many copies of a tet operator (tetO) binding site in both a plasmid and genomic context can competitively bind to the tet-transcriptional activator (tTA). These tetO decoys were able to convert the graded dose–response between tTA and target promoters to a steeper, threshold response.Using a model to analyze these results indicated that the qualitative change in response was due to stronger binding between tTA and the tetO decoy sites versus the promoter sites at low tTA levels. We confirmed this prediction using quantitative chromatin immunoprecipitation.Repetitive regions of DNA that constitute a significant fraction of many organisms’ genomes often contain TF binding sites of variable number. Our findings raise the intriguing possibility that these decoy sites may have an indirect regulatory role.