Fig. 4. The affinity of proteins to importin contributes significantly to their ordering of nuclear entry in early development.
a Estimation of proteome-wide affinity to importin α/β. We quantified changes in protein abundance associated with importin beads among conditions with varying amounts of RanQ69L. Abundance of known importin α/β substrates53, including histones, decreases with increasing RanQ69L concentration. Large dots represent the median protein fraction of a protein subgroup at each RanQ69L concentration, while small dots represent measurements for individual proteins. We applied a linear fit for each protein with a fixed y-intercept and used the slope to proxy for a protein’s affinity to importin. b Scatter plot of triplicate affinity proxy measurements from experiments outlined in (a). We integrated these measurements to one dimension using cross-validated canonical correlation analysis49. c Importin affinity can explain a significant fraction of the timing of nuclear entry in early development. The scatter plot shows Tembryo1/2 versus importin α/β affinity proxy. The observed Pearson correlation suggests that importin affinities can explain >46% of the variance of the timing of nuclear entry or NLS containing proteins in early embryonic development. d Schematic of our proposed model in which the differential affinity of proteins to importin controls the timing of genomic access in embryonic development. A high-affinity protein titrates into the nucleus faster than a low-affinity protein, resulting in the corresponding DNA access of proteins. This ordering could determine the timing for the onset of downstream transcription. e Simulation of the model proposed in (d). We model competitive binding of substrates with varying affinity to a limiting number of importin. The proposed model provides a simple explanation for the timing of protein access to the embryonic genome in early development.