Single molecule biophysics in living organisms

Current research:

In higher organisms, the early phase of embryonic development is driven by maternally inherited protein and mRNA. After a species-dependent number of cell cycles the zygotic genome is activated and its genes are transcribed (zygotic genome activation, ZGA). We investigate the molecular mechanisms underlying ZGA in live developing Zebrafish embryos at the single molecule level by reflected light-sheet microscopy. Our time and space resolved kinetic measurements allow us to build quantitative models of ZGA.

Published Projects:

→ Embryo development

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. 
http://export.arxiv.org/abs/1710.03539