Reverse engineering of the transcriptional network downstream of RAF/MAPK signaling

丝裂原活化蛋白激酶(MAPK)信号转导通路通过诱导数百个靶基因调控多种细胞功能。虽然这些靶程序是已知的，但协调这些靶基因表达的转录网络尚不清楚。在这里，我们建议利用基因组编辑、单细胞基因组学和计算网络重建方法的进展来反向工程MAPK下游的转录网络。具体地说，我们将把不同的汇集CRISPR方法与有针对性的单细胞转录结合起来，为50个MAPK依赖的转录因子生成扰动-响应图。然后，该数据将被用作网络重建方法的输入，该方法被称为“响应逻辑”，该方法使用答案集解算器的能力来重建与扰动-响应图一致的网络。专门设计的组合扰动将被用来验证和完善这些网络，并识别和验证冗余和协同转录因子。

Mitogen-activated protein kinase (MAPK) signal transduction controls a variety of cellular functions via the induction of hundreds of target genes. While these target programs are known, the transcriptional network that orchestrates the expression of these target genes is not understood. Here we propose to use the technical advances in genome editing, single cell genomics and advances in computational network reconstruction approaches to reverse engineer the transcriptional network downstream of MAPK. Specifically, we will combine different pooled CRISPR approaches with targeted single cell transcriptomes to generate perturbation-response maps for 50 MAPK dependent transcription factors. This data will then be used as input for a network reconstruction approach termed “response logic” that uses the power of answer set solvers to reconstruct networks that agree with the perturbation-response maps. Specifically designed combinatorial perturbations will be used to validate and refine those networks and to identify and validate redundant and synergistic transcription factors.