Live-Cell Imaging Reveals Enhancer-dependent Sox2 Transcription in the Absence of Enhancer Proximity

Abstract

ABSTRACTEnhancers are important regulatory elements that can control gene activity across vast genetic distances. However, the underlying nature of this regulation remains obscured because it has been difficult to observe in living cells. Here, we visualize the spatial organization and transcriptional output of the key pluripotency regulatorSox2and its essential enhancerSox2Control Region (SCR) in living embryonic stem cells (ESCs). We find thatSox2and SCR show no evidence of enhanced spatial proximity and that spatial dynamics of this pair is limited over tens of minutes.Sox2transcription occurs in short, intermittent bursts in ESCs and, intriguingly, we find this activity demonstrates no association with enhancer proximity, suggesting that direct enhancer-promoter contacts do not drive contemporaneousSox2transcription. Our study establishes a framework for interrogation of enhancer function in living cells and supports an unexpected mechanism for enhancer control ofSox2expression that uncouples transcription from enhancer proximity.