Transcriptional control in plants

Abstract

Arabidopsis gene expression is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location, and transcriptional strength of their ADs. To address this gap, we experimentally identified Arabidopsis ADs on a proteome-wide scale using a yeast library approach, finding that over half of the Arabidopsis TFs carry an AD. We annotated 1,553 ADs, the vast majority of which were previously unknown. We used the dataset generated to develop a neural network to accurately predict ADs and to identify sequence features necessary to recruit coactivator complexes. We uncovered six distinct sequence feature combinations that resulted in activation activity, providing a framework to interrogate activation domain sub-functionalization. Furthermore, we identified ADs within the ancient AUXIN RESPONSE FACTOR (ARF) family of TFs, uncovering conservation of AD positioning in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examination of function within intrinsically disordered regions, and a predictive model of ADs.