Characterizing the ribosome code controlling gene expression and cell fate specification

 描述（由申请人提供）：在空间和时间上控制基因表达在使细胞能够“知道”它们在发育中的胚胎中的位置以及变成什么方面起着重要作用，这一过程通常被称为细胞特化。几十年的研究表明，在转录和转录后水平上，基因表达的调控有许多层次，它们协调这一过程。相反，基因表达的翻译调控却很少受到实验的关注。最值得注意的是，流行的教条是，在蛋白质生产的水平上，核糖体-尽管是一个非常复杂的分子机器-在翻译mRNA方面具有组成性而不是调节性功能。我们的研究结果出乎意料地揭示了胚胎发育和组织模式的基本方面是由核糖体的高度调节功能控制的。重要的是，我们已经表明，“专门的核糖体”窝藏一个独特的组成或活动是至关重要的哺乳动物身体计划的形成所需的，并直接在何处和何时关键发育调节因子，如Hox基因，表达。此外，我们的研究已经确定了新的RNA调节子嵌入在关键发育调节因子的5 'UTR中，这些调节因子通过核糖体赋予更大的基因调节潜力。在这项提案中，我们将采取高度多学科的方法，首次系统和全面地定义核糖体组成在细胞分化过程中如何变化。具体而言，我们假设核糖体的组成是高度动态的干细胞分化过程中，赋予新的调控潜力的转录后基因表达的基础快速和动态的细胞命运的决定。在本提案中，我们将通过两个具体目标来解决这一假设。在目标1中，我们将采用最先进的质谱法系统地检查胚胎干细胞中的核糖体组成，并在其分化为神经祖细胞和心肌细胞的功能表征核糖体异质性对基因调控的贡献。在目标2中，我们将采用一种高功能的方法来定义转录本的库，这些转录本选择性地依赖于特定的核糖体成分，以便在细胞命运规范过程中准确表达。总之，这些研究将为控制基因表达带来新水平的监管特异性，指导细胞命运决定，反映细胞命运规范背后的监管电路的范式转变。

 DESCRIPTION (provided by applicant): Control of gene expression in space and time plays an important role in enabling cells to "know" where they are in the developing embryo and what to become, a process often referred to as cellular specification. Decades of research have demonstrated numerous layers of regulation in control of gene expression, at both the transcriptional and post-transcriptional level, which coordinate this process. Translational contro of gene expression has, on the contrary, received less experimental attention. Most notably, the prevailing dogma is that at the level of protein production, the ribosome -although an immensely complex molecular machine- possesses a constitutive rather than regulatory function in translating mRNAs. Our findings unexpectedly reveal that fundamental aspects of embryonic development and tissue patterning are instead controlled by a highly regulatory function of the ribosome. Importantly, we have shown that "specialized ribosomes" harboring a unique composition or activity are critically required for the formation of the mammalian body plan and direct where and when key developmental regulators, such as Hox genes, are expressed. In addition, our research has identified novel RNA regulons embedded within the 5'UTRs of key developmental regulators that confer greater gene regulatory potential by the ribosome. In this proposal we will undertake a highly multidisciplinary approach to systematically and comprehensively define for the first time how ribosome composition changes during cell differentiation. Specifically, we hypothesize that the composition of the ribosome is highly dynamic during stem cell differentiation to confer novel regulatory potential to post-transcriptional gene expression underlying rapid and dynamic cell fate decisions. In this proposal we will address this hypothesis through two specific aims. In Aim 1 we will employ state-of-the-art mass spectrometry to systematically examine ribosome composition in embryonic stem cells and during their differentiation into neural progenitors and cardiomyocytes to functional characterize the contributions of ribosome heterogeneity towards gene regulation. In Aim 2 we will undertake a highly functional approach to define the repertoire of transcripts that selectively rely on specific ribosome components for their accurate expression during cell fate specification. Together, these studies will bring to bear a new level of regulatory specificit for control of gene expression that instructs cell fate decisions reflecting a paradigm-shift in th regulatory circuitry underlying cell fate specification.