Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Transcription factors (TFs) control gene expression by interacting with DNA and cofactors to regulate transcription. Human TF genes produce multiple protein isoforms with altered DNA binding domains, effector domains, and other protein regions. The global extent to which this results in functional differences between TF isoforms of the same gene remains unknown. Here, we systematically tested 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Compared to the reference isoform, two-thirds of alternative TF isoforms exhibit differences in their molecular activities, which often cannot be predicted from sequence alone. We observed two primary categories of alternative TF isoforms: “rewirers” and “negative regulators”, both of which are associated with differentiation and cancer. Our results support a model wherein the relative expression levels of and interactions between TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies. 5 full-length TF isoforms belonging to 2 TF genes were assayed by protein binding microarrays (PBM) as part of the above work.