Why do transcription factors bind what they bind when they bind?

Introduction

Transcription factor binding is orchestrated by a complex interplay between DNA sequence, chromatin composition, protein interactions, and transcription factor concentration. These regulatory features determine the binding kinetics: how long it takes for a certain amount of transcription factor to associate, and subsequently dissociate from specific binding sites. These kinetics are in turn determined by the thermodynamic properties of each interaction.

Current Limitations

It is currently not possible to measure the biochemical kinetics of transcription factor binding across the chromatinized genome inside the nucleus of a cell. To understand why a transcription factor binds to a specific chromatin:DNA-sequence context in a specific cellular state at a specific time, we need to measure how chromatin and DNA influence the biochemical parameters that underpin transcription factor binding. This gap in knowledge limits our functional understanding of why a binding event occurs, and it hampers accurate predictions of transcription factor binding.

Proposed Solution

Here, I will establish a novel proteomics and genomics toolkit to decipher the regulation of transcription factor binding kinetics to the chromatinized genome. I will resolve interactome- and genome-wide binding kinetics of three lung-cancer-associated transcription factors.

Objectives

By delineating the following, I aim to obtain a quantitative understanding of how the proteome composition, epigenetic landscape, and genetic code dictate transcription factor binding:

1. Association and dissociation rates
2. Changes in disorder
3. Binding energy of all binding events across the genome

Expected Outcomes

Finally, I will build predictive binding models to engineer cell-state-specific transcription factor binding profiles. Together, this will transform our knowledge about transcription factor binding into a functional understanding where instead of observing, we understand why each binding event occurs when it occurs, and how we can steer these events.