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.