Adrian Sanborn (Stanford University)| Benjamin Yeh (Stanford University)| Jordan Feigerle (Stanford University)| Cynthia Hao (Stanford University)| Raphael Townshend (Stanford University)| Erez Aiden (Baylor College of Medicine, Rice University)| Ron Dror (Stanford University)| Roger Kornberg (Stanford University)
Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity ("fuzzy" binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology.
"A quantitative screen identifies 150 activation domains from all yeast transcription factors (TFs) (A) Schematic of the activation assay. (B) Pooled screen for activation domains (ADs). (C) Histogram of activation measured for 7460 tiles spanning all yeast TFs. (D) Activation data for tiles spanning three example proteins. (E) Heatmap showing the mean activation at each position of the 60 TFs with the strongest ADs. (F) Histogram of the number of ADs in each TF."
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