Promoter strength and position govern promoter competition

Competition between promoters within a shared regulatory landscape has been implicated in development and disease, but the determinants of promoter competition have not been systematically studied. Here, we use a synthetic platform to introduce diverse promoters at defined genomic sites within the Sox2 locus and measure how these inserted promoters attenuate activity of the endogenous promoter. We find that reduction in endogenous Sox2 transcription is correlated with the strength of the inserted promoter. Transcription from the inserted promoter is required for competition, with longer transcript resulting in more competition. Furthermore, competition is dependent on the location of the inserted promoter, but independent of cohesin mediated loop extrusion. Lastly, we encounter silencing of the de novo inserted promoter by HUSH, which counteracts competition. Together, our work uncovers the rules governing promoter competition, highlights its impact on tuning gene expression levels, and suggests a role for RNA in mediating this process.