Transcription factors (TFs) exert their regulatory influence through the binding of enhancers, resulting in coordination of gene expression programs. Active enhancers are often characterized by the presence of short, unstable transcripts termed enhancer RNAs (eRNAs). While their function remains unclear, we demonstrate that eRNAs are a powerful readout of TF activity. We infer sites of eRNA origination across hundreds of publicly available nascent transcription data sets and show that eRNAs initiate from sites of TF binding. By quantifying the colocalization of TF binding motif instances and eRNA origins, we derive a simple statistic capable of inferring TF activity. In doing so, we uncover dozens of previously unexplored links between diverse stimuli and the TFs they affect.

转录因子（TF）通过增强子的结合发挥其调节影响，从而协调基因表达程序。活性增强子的特征通常是存在短的、不稳定的转录物，称为增强子 RNA (eRNA)。虽然它们的功能仍不清楚，但我们证明 eRNA 是 TF 活性的强大读数。我们通过数百个公开可用的新生转录数据集推断出 eRNA 起源位点，并表明 eRNA 从 TF 结合位点起始。通过量化 TF 结合基序实例和 eRNA 起源的共定位，我们得出了能够推断 TF 活性的简单统计数据。在此过程中，我们发现了多种刺激与其影响的转录因子之间的数十种先前未探索过的联系。