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

RAF/MAPK 信号下游转录网络的逆向工程

• 批准号: 530963080
• 负责人: Professor Dr. Nils Blüthgen
• 金额: --
• 依托单位: Institut für Molekulare Medizin
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/530963080?language=en
• 关键词: Reverse; engineering; transcriptional; network; downstream

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.

丝裂原激活蛋白激酶 (MAPK) 信号转导通过诱导数百个靶基因来控制多种细胞功能。虽然这些目标程序是已知的，但协调这些目标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、单细胞基因组学的技术进步和计算网络重建方法的进步来对 MAPK 下游的转录网络进行逆向工程。具体来说，我们将结合不同的 CRISPR 方法与靶向单细胞转录组，生成 50 个 MAPK 依赖性转录因子的微扰响应图。然后，该数据将用作称为“响应逻辑”的网络重建方法的输入，该方法利用答案集求解器的功能来重建与扰动响应图一致的网络。特别设计的组合扰动将用于验证和完善这些网络，并识别和验证冗余和协同转录因子。