BPS2026 – Decoding YAP dynamics through charge-mediated co-condensates

YAP is a transcriptional regulator that controls several cell fate decisions, including proliferation, pluripotency, and differentiation. Using an optogenetic approach, we previously demonstrated that cells leverage YAP concentrations and dynamics to differentially control gene programs underlying these cellular decisions in stem cells. Yet, how YAP levels and dynamics are decoded by the gene regulatory machinery has remained unclear. Here, we probe the role of transcriptional condensates as molecular logic gates for temporal decoding. Leveraging light-sheet single-molecule imaging, synthetic condensates, and IDR sequence analysis, we demonstrate that YAP forms co-condensates with the transcriptional regulator Mediator that are well-suited as temporal decoders. We find that YAP condensate formation is driven by electrostatic interactions with the oppositely charged transcriptional regulator Mediator. IDR grammar analysis and protein engineering demonstrate that the interaction is mediated through YAP’s charge pattern, which specifically interacts with the opposing charge pattern of Mediator. The co-condensation of both proteins drives transcriptional activation but is counteracted by delayed negative feedback from the transcriptional output. The resulting adaptive transcriptional response is well-suited to decode pulsatile YAP dynamics, effectively acting as a sensor. Our work provides a new mechanism for decoding transcription factor dynamics and highlights the necessity of molecular-resolution approaches for probing core concepts of phase separation, which easily evade conventional techniques.