Decreasing nuclear volume concentrates DNA and enforces transcription factor-chromatin associations during Zebrafish genome activation

Zygotic genome activation (ZGA), the onset of transcription after initial quiescence, is a major developmental step in many species, which occurs after ten cell divisions in Zebrafish embryos. How transcription factor-chromatin interactions evolve during early development to support ZGA is largely unknown. We established single molecule tracking in live developing Zebrafish embryos using reflected light-sheet microscopy to visualize the general transcription factor TATA-binding protein (TBP), and developed a novel data acquisition and analysis scheme to extract kinetic information during fast cell cycles. The chromatin-bound fraction of TBP increases during early development, compatible with increasing transcriptional activity. By quantifying TBP and DNA concentrations and their binding kinetics, we device a physical model of how the nuclear volume, which decreases during early development, enhances TBP-chromatin associations. Our single molecule data suggest that the shrinking nucleus is a major driving force and timer of ZGA in Zebrafish embryos.