Toward defining the transcriptional ecosystem

* 理由。在环境扰动之后，细胞必须迅速做出反应，以确保适当的基因反应。基因应答依赖于转录因子将转录机器和辅调节因子募集到调节区域。在细胞核中，基因组结构在形成局部微环境的多个基因的调节区域之间产生接近。最近的证据表明，转录辅调节因子是高度移动的在这些封闭的微环境。这在概念上让人联想到自然界中的生态系统，在那里多个种群创造动态的相互作用，以共享资源和维持稳态。转录辅助调节子库是否在相连的基因组之间分配和交换是一个悬而未决的问题。目标.我们研究计划的长期目标是证明共享相同物理环境的基因之间存在转录生态系统平衡。 在最初的5年里，我们的目标是确定转录辅调节子是一组基因中的移动的实体。我们的中心假设是，转录辅助调节基因之间的交易，以维持对环境扰动的反应。为了测试我们的模型，我们提出了两个具体的目标：* 目标1确定一组基因对伴随信号的反应。对资源的竞争是自然生态系统的一个重要特征。利用环境扰动，我们将研究基因组如何对伴随信号作出反应。这将使我们能够确定竞争和协同基因环境的存在。目的2确定转录资源的作用范围。转录机制和辅助调节因子是高度动态的实体。我们将利用它们的移动性来识别共享转录资源的相关基因。为此，我们将靶向与BirA融合的dCas9，以生物素化指定启动子周围的蛋白质，并测量向连接基因的传播。预期成果。我们将建立一个新的概念框架，其中基因是生态系统的一部分，在这个生态系统中，转录辅调节因子是限制性的，因此从一个基因到另一个基因。我们将确定是否存在转录机制和辅助调节因子的竞争，这对于理解细胞如何整合伴随信号至关重要。我们将通过实验来证实基因间辅调节子的移动。最后，我们将确定是否高表达基因被用作转录资源库，以维持基因反应。* 影响。有了这些发现，我们将把我们的研究领域从半稳定的转录模型转移到生化平衡。这将重新定义直接和间接靶点的概念，因为基因不必直接被激活的转录因子所占据。

***Rationale. Following environmental perturbations, cells must quickly react to ensure a proper gene response. Gene responses depend on transcription factor recruiting the transcription machinery and coregulators to regulatory regions. In the nucleus, the genome architecture creates proximity between regulatory regions of multiple genes forming local microenvironments. Recent evidence suggests that transcription coregulators are highly mobile within these enclosed microenvironments. This is conceptually reminiscent of ecosystems found in nature where multiple populations create dynamic interplays to share resources and maintain homeostasis. Whether or not a pool of transcription coregulators is assigned and traded between groups of connected genes is an open question.******Objectives. The long-term goal of our research program is to demonstrate the existence of transcriptional ecosystem equilibriums between genes sharing the same physical environment. During the first 5 years, our goal will be to establish that transcription coregulators are mobile entities within a group of genes. Our central hypothesis is that transcription coregulators are traded between genes to sustain the response to environmental perturbations. To test our model, we are proposing two specific objectives:******Objective 1 Determine the response of group of genes to concomitant signals. Competition for resources is an important feature of natural ecosystems. Using environmental perturbations, we will investigate how group of genes react to concomitant signals. This will allow us to determine the presence of competitive and synergistic gene environments.***Objective 2 Establish the range of action of the transcriptional resources. Transcription machinery and coregulators are highly dynamic entities. We will use their mobility to identify connected genes sharing transcriptional resources. To do so, we will target the dCas9 fused to BirA to biotinylate proteins surrounding designated promoters and measure spreading to connected genes.******Expected Outcomes. We will establish a new conceptual framework where genes are part of an ecosystem in which transcription coregulators are limiting and therefore travel from gene to gene. We will determine if competition for transcription machinery and coregulators exist which will be crucial to understand how a cell integrates concomitant signals. We will experimentally confirm the travelling of coregulators between genes. Lastly, we will determine if highly expressed genes are used as a transcriptional resources reservoir to sustain gene responses. ******Impact. With these discoveries, we will move our research field from semi-stable transcriptional models to biochemical equilibriums. This will redefine the notion of direct and indirect targets since a gene will not have to be directly occupied by an activated transcription factor to be regulated.**