PDF(Pubmed)
Abstract：
In any given cell type, dozens of transcription factors (TFs) act in concert to control the activity of the genome by binding to specific DNA sequences in regulatory elements. Despite their considerable importance in determining cell identity and their pivotal role in numerous disorders, we currently lack simple tools to directly measure the activity of many TFs in parallel. Massively parallel reporter assays (MPRAs) allow the detection of TF activities in a multiplexed fashion; however, we lack basic understanding to rationally design sensitive reporters for many TFs. Here, we use an MPRA to systematically optimize transcriptional reporters for 86 TFs and evaluate the specificity of all reporters across a wide array of TF perturbation conditions. We thus identified critical TF reporter design features and obtained highly sensitive and specific reporters for 60 TFs, many of which outperform available reporters. The resulting collection of \"prime\" TF reporters can be used to uncover TF regulatory networks and to illuminate signaling pathways.
摘要：
在任何给定的单元格类型中，数十种转录因子（TFs）通过与调节元件中的特定DNA序列结合来共同控制基因组的活性。尽管它们在确定细胞身份方面相当重要，并且在许多疾病中发挥关键作用，我们目前缺乏简单的工具来直接并行测量许多TFs的活性。大规模平行报告分析（MPRAs）允许以多重方式检测TF活性；然而，我们缺乏基本的理解来合理设计许多TFs的敏感记者。这里,我们使用MPRA系统地优化86个TF的转录报告基因,并评估所有报告基因在多种TF扰动条件下的特异性.因此，我们确定了关键的TF报告子设计特征，并获得了60个TF的高度敏感和特定的报告子，其中许多优于现有记者。所得的“prime”TF报告基因的集合可用于揭示TF调节网络并阐明信号通路。
结论：针对86个TFs的转录报告基因的系统设计和优化TF特异性报告基因设计优化规则的表征在广泛的TF扰动中评估报告基因TF特异性的鉴定具有优化性能的60个“prime”TF报告基因的集合。
结论：针对86个TFs的转录报告基因的系统设计和优化TF特异性报告基因设计优化规则的表征在广泛的TF扰动中评估报告基因TF特异性的鉴定具有优化性能的60个“prime”TF报告基因的集合。
