@article{896ed88fa99e49dfb1dc5eedcb475d5b,
title = "Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains",
abstract = "Acidic activation domains are intrinsically disordered regions of the transcription factors that bind coactivators. The intrinsic disorder and low evolutionary conservation of activation domains have made it difficult to identify the sequence features that control activity. To address this problem, we designed thousands of variants in seven acidic activation domains and measured their activities with a high-throughput assay in human cell culture. We found that strong activation domain activity requires a balance between the number of acidic residues and aromatic and leucine residues. These findings motivated a predictor of acidic 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 previously unidentified ones. Our results support a flexible acidic exposure model of activation domains in which the acidic residues solubilize hydrophobic motifs so that they can interact with coactivators. A record of this paper's transparent peer review process is included in the supplemental information.",
keywords = "activation domain, all-atom simulations, deep mutational scanning, genomic method development, high-throughput mutagenesis, intrinsically disordered protein, intrinsically disordered region, transcription factor",
author = "Max Staller and Eddie Ramirez and Kotha, {Sanjana R.} and Holehouse, {Alex S.} and Pappu, {Rohit V.} and Cohen, {Barak A.}",
note = "Funding Information: We thank Minhee Park and Ahmed Khalil for sharing the synthetic DBD and promoter sequence ahead of publication; Kiersten Ruff, Avi Ramu, and Nicole Rockweiler for bioinformatics help; Brittany Pioso for their help with the cartoons; Jessica Hoisington-Lopez and MariaLynn Crosby for DNA sequencing. We thank members of the Cohen Lab and Thomas Graham for helpful discussions and comments on the manuscript. M.V.S. was supported by the Burroughs Wellcome Fund Postdoctoral Enrichment Program, American Cancer Society Postdoctoral Fellowship, NIGMS K99131022, and NSF 2112057. E.R. was supported by the McDonnell Genome Institute Opportunities in Genomics Research Program under grant NIH-R25HG006687. This work was supported by grants from the National Institutes of Health, NINDS 5R01NS056114 to R.V.P. NIGMS R01GM092910 to B.A.C. and the Children's Discovery Institute CDI-LI-2018-765 to B.A.C. M.V.S. and B.A.C. designed the project and wrote the manuscript. M.V.S. and E.R. collected the data. M.V.S. E.R. S.R.K. and A.S.H. analyzed the data. R.V.P. and B.A.C. interpreted the data. All authors edited the manuscript. The authors declare no competing interests. One or more of the authors of this study self-identifies as an underrepresented ethnic minority in science. One or more of the authors of this study received support from a program designed to increase minority representation in science. Funding Information: We thank Minhee Park and Ahmed Khalil for sharing the synthetic DBD and promoter sequence ahead of publication; Kiersten Ruff, Avi Ramu, and Nicole Rockweiler for bioinformatics help; Brittany Pioso for their help with the cartoons; Jessica Hoisington-Lopez and MariaLynn Crosby for DNA sequencing. We thank members of the Cohen Lab and Thomas Graham for helpful discussions and comments on the manuscript. M.V.S. was supported by the Burroughs Wellcome Fund Postdoctoral Enrichment Program, American Cancer Society Postdoctoral Fellowship, NIGMS K99131022, and NSF 2112057 . E.R. was supported by the McDonnell Genome Institute Opportunities in Genomics Research Program under grant NIH - R25HG006687 . This work was supported by grants from the National Institutes of Health , NINDS 5R01NS056114 to R.V.P., NIGMS R01GM092910 to B.A.C., and the Children{\textquoteright}s Discovery Institute CDI-LI-2018-765 to B.A.C. Publisher Copyright: {\textcopyright} 2022 The Authors",
year = "2022",
month = apr,
day = "20",
doi = "10.1016/j.cels.2022.01.002",
language = "English",
volume = "13",
pages = "334--345.e5",
journal = "Cell Systems",
issn = "2405-4712",
number = "4",
}