Physical Genomics: From Single-Cell to Evolutionary Dynamics

 描述(申请人提供)：DNA测序的出现表明，基因组是我们掌握的生物功能和进化的最具启发性的窗口之一。例如，在微生物世界，基因组测序告诉我们，横向基因转移是导致毒力和抗生素耐药性出现的关键过程，在传染病的背景下，这是一个重要且日益令人担忧的问题。在免疫系统的细胞中，为了应对传染性病原体的巨大多样性，人类基因组经历了一个剪切粘贴过程，从而产生了大量独特的抗体。细胞对环境变化的反应时间也要快得多。不同的基因在不同的时间和不同的位置被激活，以响应其化学和物理环境的瞬时变化。这些调控决定的范围从表达关于利用环境中哪种碳源的代谢偏好到对人类健康至关重要的选择，例如细胞是否会进入不受控制的增殖状态或表达抗生素耐药性基因。然而，关于基因组是如何工作的，我们仍然有很多不了解的地方。即使是在对细菌了解最深的生物体中，如大肠杆菌，我们仍然完全不知道它的一半基因是如何调控的。就像蛋白质结构只能给出一大堆不同构象的单一结构快照一样，基因组也是动态的。此外，与蛋白质类似，序列分析几乎永远不足以告诉我们基因是如何在其生理环境中被调节和利用的。这里提出的研究集中在基因组动力学的三个具有挑战性的重要方面：(I)使用物理模型和单细胞显微镜来开发不同生物体之间基因如何转移的规则的机械论观点，这一过程不仅对微生物的长期进化至关重要，而且对传染病的短期出现也至关重要。(2)基于测序和建模的方法的发展，使我们不仅能够确定我们没有任何调控信息的基因是如何被调控的，而且还能够定量地描述它们的输入-输出功能。(3)单细胞定量研究，将这些转录输入输出功能与细胞对抗生素或渗透性休克等各种环境侮辱的生理反应联系起来。这些努力中的每一项都旨在提供对基因如何转移、调节和表达以执行生理功能的序列水平的理解。

 DESCRIPTION (provided by applicant): The advent of DNA sequencing has shown genomes to be one of the most revealing windows onto biological function and evolution at our disposal. For example, in the microbial world, genome sequencing has taught us that lateral gene transfer is a key process responsible for the emergence of virulence and antibiotic resistance, an important and increasing concern in the context of infectious diseases. In response to the enormous diversity of infectious pathogens, in the cells of the immune system, the human genome undergoes a cut-and-paste process that leads to a huge array of unique antibodies. Cells respond to changes in the environment on much faster time scales as well. Different genes are turned on at different times and in different places in response to instantaneous changes in their chemical and physical environment. These regulatory decisions range from the expression of metabolic preferences about which carbon source in an environment to exploit to choices critical to human health, such as whether cells will enter a state of unchecked proliferation or express antibiotic resistance genes. Yet, there remains much that we don't understand about how genomes work. Even in the best understood of organisms such as the bacterium E. coli, we remain completely ignorant of how half of its genes are regulated. Just as protein structures give only a single structural snapshot from a huge array of different conformations, genomes are dynamic too. Further, in analogy with proteins, analysis of sequence is almost never enough to tell us how genes are regulated and exploited in their physiological setting. The research proposed here focuses on three challenging and important aspects of genome dynamics: (i) The use of physical models and single-cell microscopy to develop a mechanistic view of the rules for how genes are transferred between different organisms, a process critical not only to the long-term evolution of microorganisms, but also to the short-term emergence of infectious diseases. (ii) The development of sequencing-based and modeling methods that permit us to determine not only how genes for which we have no regulatory information are regulated, but also to quantitatively characterize their input-output functions. (iii) Quantitative single-cell studies that relate these transcriptional input-output functions to the physiological response of cells to various environmental insults such as antibiotics or osmotic shock. Each of these efforts aims to provide a sequence-level understanding of how genes are transferred, regulated and expressed to carry out physiological functions.