Fig. 2.

Temporal modes of organizing mammalian transcriptional dynamics. a Modulating transcription through TF binding and target search, in which a TF molecule undergoes “facilitated diffusion” by partitioning its movement between free 3D diffusion (purple) and transient 1D sliding along the DNA (blue) until the specific target sites are located and to which the TF stays bound for a long time (red). b An example of the physiological consequence of TF binding dynamics, in which the long-lived bound fraction of Sox2 in a blastomere of a four-cell embryo predicts the bias with which this blastomere will contribute to the inner mass of the embryo subsequently. c Modulating transcription through pulsatile production or “bursts” of mRNAs, as a consequence of stochastic switching of the gene between the “on” and ”off” states. d Widely different Nanog expression among a population of mouse ES cells as revealed by smFISH. In contrast to the sparse Nanog molecules present in the two lower cells, multiple spots where bursts of Nanog transcription took place (indicated by red arrowheads) are discernible in the top cell. Dotted lines delineate nuclear boundaries. Adapted from [66] (a, b) with modifications