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

Cell systems Pub Date : 2024-07-17 Epub Date: 2024-06-11 DOI:10.1016/j.cels.2024.05.007
Niklas F C Hummel, Kasey Markel, Jordan Stefani, Max V Staller, Patrick M Shih
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Abstract

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.

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系统鉴定植物和酵母中非转录因子蛋白的转录激活结构域。
转录因子可通过激活结构域促进基因表达。全基因组筛选系统地绘制了转录因子的激活结构域,但没有绘制非转录因子蛋白(如染色质调节因子和辅助激活因子)的激活结构域。为了填补这一知识空白,我们利用激活结构域预测工具 PADDLE 分析了拟南芥和酿酒酵母的蛋白质组。我们筛选了这两个物种中超过 800 个非转录因子基因的 18,000 个预测激活结构域,证实 89% 的候选蛋白质含有活性片段。我们的工作使我们能够将数百种核蛋白注释为推定的辅助激活因子,其中许多在植物中从未被赋予任何功能。对肽序列组成的分析揭示了关键氨基酸的分布是如何决定活性的。最后,我们验证了简短的 "通用 "激活结构域,其性能与用于基因组工程的最先进激活结构域相当。我们的方法能够在全基因组范围内发现和注释能够在不同真核生物中发挥作用的激活结构域。
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