Chromatin Structure and Gene Expression

Division Of Basic Sciences - Nci

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Abstract

Single Molecule Tracking (SMT) allows the study of TF dynamics in the nucleus, giving important information regarding the search and binding behavior of these proteins with chromatin in vivo. However, how TFs navigate within the intricate nuclear environment to find and bind their response elements on chromatin, recruit the transcription machinery, and ultimately regulate gene expression remains largely unknown. By the implementation of proper photobleaching kinetics, theory-based models and an unbiased model selection approach, we revealed a new model of TF dynamics where TFs binding times are power-law distributed. Previous models suggested that TFs bound either non-specifically or specifically, with each mode of binding having their own distribution that was largely discrete from the other. The power-law model, on the other hand, indicates that TFs bind not discretely in these two modes, but with a continuous distribution from fast to very slow kinetics. These results are aligned with the theoretical underpinnings of TF motions in the crowded nuclear space and exploration of a complex DNA space To fully understand the broad distribution of TFs binding affinities, we explored how the nuclear microenvironment affects the binding of TFs to chromatin. We found that TFs present two types of binding: local confinement (also designated State 2), and direct binding to chromatin (also designated as State 1). We showed that the power law distribution of binding times is due to TFs confinement and heterogeneity in binding affinity to chromatin.