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

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, 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.转录因子（Transcription factors）可通过激活结构域（activation domains）促进基因表达。全基因组筛选已系统性地定位了转录因子中的激活结构域，但尚未在非转录因子蛋白（如染色质调控因子（chromatin regulators）、辅激活因子（coactivators））中完成此类图谱绘制。为填补这一研究空白，我们借助激活结构域预测工具PADDLE，对拟南芥（Arabidopsis thaliana）与酿酒酵母（Saccharomyces cerevisiae）的蛋白质组展开分析。我们从两个物种的800余个非转录因子基因中筛选出18000个预测激活结构域，证实其中89%的候选蛋白携带活性片段。本研究可将数百个核蛋白注释为推定辅激活因子，其中诸多蛋白在植物中从未被赋予任何功能。对肽段序列组成的分析揭示了关键氨基酸的分布如何决定其活性。最后，我们验证了短小的“通用”激活结构域，其性能可与用于基因组工程的前沿激活结构域相媲美。我们的方法可实现在全基因组范围内发现并注释可在多种真核生物中发挥功能的激活结构域。