Sequence properties of human acidic transcriptional activation domains

Acidic activation domains are intrinsically disordered regions of transcription factors that bind coactivators. The intrinsic disorder and low evolutionary conservation of activation domains have made it difficult to identify the sequence features controlling AD activity. To address this problem, we designed thousands of variants in seven acidic activation domains and measured their activities with a new high-throughput assay in human cell culture. We found that strong activation domain activity required a balance between the number of acidic residues and aromatic and leucine residues. These findings motivated a predictor of activation domains that scans the human proteome for clusters of aromatic and leucine residues embedded in regions of high acidity. This predictor identifies known activation domains and accurately predicts new ones. Our results support a flexible model of activation domains in which acidic residues solubilize hydrophobic motifs so that they can interact with coactivators. Overall design: To measure transcriptional activation domain activity, we used FACS to separate cells with different GFP levels of a reporter construct. We sequenced the barcodes attached to each activation domain in each sorted population.