Promoter strength and position govern promoter competition via transcript-dependent insulation [Micro-C]

Here, we introduce diverse promoters into defined genomic sites within the Sox2 locus and measure how these insertions attenuate endogenous Sox2 expression. We find that the level of 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. The inserted active promoter and its associated transcriptional unit function as an insulator, rendering competition position-dependent. Finally, we observe HUSH-mediated silencing of the inserted promoters, which counteracts competition.