Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis

The three-dimensional folding of chromosomes is essential for nuclear functions such as DNA replication and gene regulation. The emergence of chromatin architecture is thus an important process during embryogenesis. To shed light on the molecular and kinetic underpinnings of chromatin architecture formation, we characterized biophysical properties of cohesin and CTCF binding to chromatin and their changes upon cofactor depletion using single-molecule imaging in live developing zebrafish embryos. We found that chromatin-bound fractions of both cohesin and CTCF increased significantly between the 1000-cell and shield stages, which we could explain through changes in both their association and dissociation rates. Moreover, increasing binding of cohesin restricted chromatin motion, potentially via loop extrusion, and showed distinct stage-dependent nuclear distribution. Polymer simulations with experimentally derived parameters recapitulated the experimentally observed gradual emergence of ..., , , # Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis [https://doi.org/10.5061/dryad.3bk3j9ks8](https://doi.org/10.5061/dryad.3bk3j9ks8) --- ## Single\_molecule\_data.zip #### Description The folder 'Single molecule data' contains mat files that include single-molecule tracking data used in the manuscript Cossmann et al., Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis. It contains subfolders labeled with the respective illumination-scheme names or analysis names used in the publication: CBD = Center-Border-Distance analysis for determining the relative positions of long-bound tracks Continous = Continous movie analysis for bound fractions and diffusion coefficients ITM = Interlaced time-lapse microscopy for relative fractions in binding time classes TACO = time-lapse alternated with continuous intervals for mo...