Large-scale mapping and mutagenesis of human transcriptional effector domains

Nicole DelRosso, Josh Tycko, Peter Suzuki, Cecelia Andrews, Aradhana, Adi Mukund, Ivan Liongson, Connor Ludwig, Kaitlyn Spees, Polly Fordyce, Michael C. Bassik and Lacramioara Bintu ()
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Nicole DelRosso: Stanford University
Josh Tycko: Stanford University
Peter Suzuki: Stanford University
Cecelia Andrews: Stanford University
Aradhana: Stanford University
Adi Mukund: Stanford University
Ivan Liongson: Stanford University
Connor Ludwig: Stanford University
Kaitlyn Spees: Stanford University
Polly Fordyce: Stanford University
Michael C. Bassik: Stanford University
Lacramioara Bintu: Stanford University

Nature, 2023, vol. 616, issue 7956, 365-372

Abstract: Abstract Human gene expression is regulated by more than 2,000 transcription factors and chromatin regulators1,2. Effector domains within these proteins can activate or repress transcription. However, for many of these regulators we do not know what type of effector domains they contain, their location in the protein, their activation and repression strengths, and the sequences that are necessary for their functions. Here, we systematically measure the effector activity of more than 100,000 protein fragments tiling across most chromatin regulators and transcription factors in human cells (2,047 proteins). By testing the effect they have when recruited at reporter genes, we annotate 374 activation domains and 715 repression domains, roughly 80% of which are new and have not been previously annotated3–5. Rational mutagenesis and deletion scans across all the effector domains reveal aromatic and/or leucine residues interspersed with acidic, proline, serine and/or glutamine residues are necessary for activation domain activity. Furthermore, most repression domain sequences contain sites for small ubiquitin-like modifier (SUMO)ylation, short interaction motifs for recruiting corepressors or are structured binding domains for recruiting other repressive proteins. We discover bifunctional domains that can both activate and repress, some of which dynamically split a cell population into high- and low-expression subpopulations. Our systematic annotation and characterization of effector domains provide a rich resource for understanding the function of human transcription factors and chromatin regulators, engineering compact tools for controlling gene expression and refining predictive models of effector domain function.

Date: 2023
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DOI: 10.1038/s41586-023-05906-y

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