PolyA/polyQ-mediated conformational rewiring regulates DNA engagement and drives aggregation in the neuronal transcription factor Ascl1

Ascl1 is a pioneer transcription factor that drives neuronal fate decisions, yet the structural basis of its activity remains elusive. Besides the basic helix-loop-helix (bHLH) domain which dimerizes with other transcription factors and binds DNA, Ascl1 contains long low-complexity intrinsically disordered regions (IDRs), including a polyA/polyQ tract of unknown function. Here we apply single-molecule FRET to generate a conformational map of full-length Ascl1 across different functional states that reveals how the polyA/polyQ tract finely tunes molecular properties. Monomeric Ascl1 is largely disordered but displays sensitive interdomain coupling between the N-terminal IDR and the bHLH domain where the polyA/polyQ tract destabilizes the latter. Heterodimerization with the transcription factor E12 not only promotes folding of the bHLH domain and high-affinity DNA binding but also relieves interdomain interactions including the low complexity polyA/polyQ tract, increasing both its extension and chain dynamics. Remarkably, deletion of the polyA/polyQ tract not only dramatically reduces non-specific DNA binding but also abolishes aggregation in vitro and increases Ascl1 abundance in human HEK293T cells. Overall, our results highlight the capacity of intrinsically disordered and low-complexity regions to impart diverse regulatory roles in transcription factors.