Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast

• Published in: Cell systems Vol. 15; no. 7; pp. 662 - 672.e4
• Main Authors: Hummel, Niklas F.C., Markel, Kasey, Stefani, Jordan, Staller, Max V., Shih, Patrick M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 17.07.2024
• Subjects: functional genomics; synthetic biology; transcription factor; transcription factor; synthetic biology; functional genomics
• ISSN: 2405-4712; 2405-4720; 2405-4720
• DOI: 10.1016/j.cels.2024.05.007

Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors but not in non-transcription factor proteins (e.g., chromatin regulators and coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. We screened 18,000 predicted activation domains from >800 non-transcription factor genes in both species, confirming that 89% of candidate proteins contain active fragments. Our work enables the annotation of hundreds of nuclear proteins as putative coactivators, many of which have never been ascribed any function in plants. Analysis of peptide sequence compositions reveals how the distribution of key amino acids dictates activity. Finally, we validated short, “universal” activation domains with comparable performance to state-of-the-art activation domains used for genome engineering. Our approach enables the genome-wide discovery and annotation of activation domains that can function across diverse eukaryotes. •Screening of >17,000 peptides with activator activity from non-transcription factors•Key residues are biased in their distribution in strongly activating peptides•Active peptides occur throughout all organelles in a plant and a fungus•Benchmarking of 51 new activating peptides in a plant gene expression system Hummel et al. utilize a yeast gene expression platform to characterize the potential of >17,000 peptides derived from non-transcription factor proteins to activate transcription. They find a positional bias of key residues in activators, curate a list of putative coactivators, and cross-validate active peptides in a plant gene expression platform.