Uncovering the regulatory logic of gene expression encoded by disordered regions

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Cellular state, identity, and function are primarily determined by the genes expressed at a given moment. Many diseases are characterized by dysregulation of gene expression, leading to inappropriate gain/loss of function that can drive proliferative growth (cancer), impede homeostasis (neurodegeneration), or rewire the immune response (viral infection). Limitations in our understanding of the complex, pleiotropic, and inherently adaptive molecular mechanisms that underlie pathological changes in gene expression are a significant barrier to our ability to design effective therapeutic strategies to alleviate these conditions. Eukaryotic gene expression is a coordinated event driven by an array of cellular processes. Among the various molecular components, transcription factors are arguably the core determinant of expression. Transcription factors are modular proteins that possess DNA-specific binding domains and facilitate the recruitment of additional co-factors that drive (or occasionally suppress) gene expression. Our understanding of how the folded DNA binding domains recognize consensus DNA binding sites is relatively mature. In contrast, we lag behind in a high-resolution understanding of other domains' various roles. Of particular interest, transcription factors are enriched for intrinsically disordered regions. These regions are often considered to play a role in driving gene expression as “activation domains” - regions that determine the strength of gene expression. However, both numerous high-throughput studies and systematic bioinformatic analyses predict that, on average, only 15% of any given transcription factor is strictly required for robust gene expression. This raises a question: what is the remaining 85% of each transcription factor IDR doing? This proposal centers on the discovery that transcription factor IDRs play a second, previously unappreciated role in coordinating gene expression. We will dissect this new role to decode the underlying molecular logic. This will involve using rational sequence design to probe the sequence-determinants of gene expression through a novel library-based approach. This will be combined with in vitro and in silico analyses to disentangle the molecular basis for our observations. Our ultimate goal is to understand how the mutations that appear in transcription factors IDRs can alter gene expression in non-intuitive and pathological ways.