Anti-phase clustering of regulatory factors shapes gene bursting

Abstract

The ability of stem cells to divide and self-renew depends on a complex choreography of molecular events that maintain the transcriptional oscillation of pluripotency genes. Only a handful of transcription factors (TFs) are necessary to preserve pluripotency and reprogram differentiated cells into stem cells. Paradoxically, while the protein players are known, the challenge remains to decipher the series of steps that TFs undertake to modulate on and off fluctuations of gene transcription. Here, we use single-molecule tracking combined with the STREAMING-tag transcriptional reporter systems to reveal temporal clustering patterns of endogenous SOX2 occupancy at the Nanog locus in relation to its nascent mRNA synthesis in live embryonic stem cells. These patterns distinctively outline multifaceted regulatory behaviours of SOX2 associated with various stages of the Nanog transcription cycle. This study exposes that SOX2 clustering activity is out-of-phase with regulatory factors that engage with transcription burst at the Nanog gene locus.