A new model for single-molecule tracking analysis reveals novel emergent properties of transcription factor dynamics

DAVID A. GARCIA; DIEGO M. PRESMAN; GREGORY FETTWEIS; CHRISTOPHER JARZYNSKI; ARPITA UPADHYAYA; GORDON L. HAGER

Cold spring Harbor, NY

Congreso; Single Biomolecules; 2018

Cold Spring Harbor laboratories

Single-molecule tracking (SMT) is a powerful technique that allows the characterization of proteindynamics in single cells. When applied to the study of transcription factor (TF) dynamics in thenucleus, important information regarding the search and binding dynamics of these proteins tochromatin in vivo can be extracted from the residence times of single TF molecules in the illuminationvolume. However, these experiments suffer from certain limitations due to photobleaching kineticsand data interpretation. The recent scientific literature does not account for an accurate correction ofphotobleaching effects, resulting in a phenomenological interpretation of the data and potentiallyleading to serious artifacts. We propose an improved method to account for photobleaching effects,theory-based models to accurately describe transcription factor dynamics, and an unbiased modelselection approach to determine the best predicting model characterizing transcription factordynamics.We propose three models of transcription factor dynamics ? i) a kinetic model that includes transitionsbetween non-specific and specific interactions with DNA, ii) a revised version of the widely usedmodel with two exponential components and iii) a new model of transcription factor searching on theDNA which results in a broad distribution of binding affinities and accounts for the power-law behaviorof transcription factor residence times.A new biological interpretation of transcriptional regulation emerges from the proposed modelschanging the paradigm of single-molecule tracking studies of TF dynamics. We use these models tointerpret the dynamics of nuclear hormone receptors and other transcription factors.