Toward defining the transcriptional ecosystem

基本原理。随着环境的扰动，细胞必须迅速作出反应，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制和共调控因子招募到调控区域。在细胞核中，基因组结构创造了多个基因调控区域之间的接近性，形成了局部微环境。最近的证据表明，转录共调控子在这些封闭的微环境中具有高度的流动性。这在概念上让人想起自然界中发现的生态系统，其中多个种群创建动态相互作用以共享资源并维持体内平衡。转录共调节因子池是否在连接基因组之间分配和交易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在共享相同物理环境的基因之间存在转录生态系统平衡。在前5年，我们的目标将是确定转录共调控子是一组基因中的移动实体。我们的中心假设是，转录共调节因子在基因之间进行交易，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目标：目标1 -确定一组基因对伴随信号的反应。资源竞争是自然生态系统的一个重要特征。利用环境扰动，我们将研究一组基因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。目标2 -建立转录资源的作用范围。转录机制和共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连接基因。为此，我们将把与BirA融合的dCas9靶向于指定启动子周围的生物素化蛋白，并测量向相关基因的传播。预期的结果。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，其中转录共调控因子受到限制，因此在基因之间传播。我们将确定是否存在转录机制和共调节因子的竞争，这对于理解细胞如何整合伴随信号至关重要。我们将通过实验证实基因间共调控子的迁移。最后，我们将确定高表达基因是否被用作维持基因反应的转录资源库。的影响。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。这将重新定义直接靶标和间接靶标的概念，因为基因不需要被激活的转录因子直接占据来调节。

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.