Rules specifying form and function of an organism are encoded in the genome. Over the years, a variety of approaches have been leveraged to elucidate the underlying programs and machinery that govern the size and form of different organs or structures. These include genetic strategies, employed to identify gene products that control developmental events, and biochemical advances that have provided molecular insights into how communication between individual cells during development is accomplished. While information theory and mathematical modeling have made inroads toward integrating genetic and molecular aspects of development, these approaches are fundamentally limited by the simple fact that most measurements that guide these applications (either genetic or biochemical) are often derived from experimental contexts that lack the spatial or temporal richness found in vivo. My research team is prepared to address a theoretical, quantitative, and computational program at Cold Spring Harbor Laboratory (CSHL) with an emphasis on in vivo cellular imaging and in situ sequencing technologies for gene expression and cell lineage analysis during development. During my postdoctoral training, I developed an in situ RNA sequencing technology that can be generally employed to determine the spatial and informational heterogeneity of gene expression in a genome-wide manner. As an independent investigator I have adapted this technology to monitor gene expression in developing tissues. These methods enable the simultaneous measurement of gene expression patterns in thousands of single cells in the context of a developing cell lineage. While simple in concept, this major advance will allow dynamic and temporal changes in gene expression to be directly tied to three-dimensional architecture, enabling the mathematical modeling of key developmental processes in the absence of prior limitations. Initially, we will focus on understanding how oscillations in gene expression pattern, including those mediated by the cell cycle, modulate growth factor signaling. Specifically, we will determine if cyclical patterns of gene expression are sufficient to generate a morphogenic field that controls the size and shape of developing structures or how these patterns contribute to the robustness of these processes in vivo. We will also determine the molecular mechanisms of gradient-associated transcriptional initiation/elongation using direct RNA sequencing in situ. Both oscillatory gene expression and morphogen gradient-associated transcriptional initiation/elongation impact aspects of cell fate commitment stem cells (important in tissue regeneration and homeostasis) and these approaches can be used to dissect the contribution of multiple genetic pathways in vivo. In summary, we have the conceptual framework, biological questions, cutting-edge technologies, and rigorous scientific environment to better characterize the biological forces driving tissue patterning and development of form and function. 1

Public Health Relevance

This project aims to understand how individual cells communicate with each other and how they interpret signals in a context-dependent manner to regulate developmental processes, such as tissue formation or organogenesis, and abnormal wound healing or tumorigenesis. It uses a novel imaging approach to visualize gene expression, functional markers, and cell lineage reporters in intact tissues with single cell resolution, and it uses modern genetic tools to activate or perturb specific signals with a precise spatial control. The overall goal is to understand rules that govern how genetic information specifies cell types and tissue structures over space and time in development. 1

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Unknown (R35)
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Special Emphasis Panel (ZRG1)
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Hoodbhoy, Tanya
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Cold Spring Harbor Laboratory
Cold Spring Harbor
United States
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Chen, Xiaoyin; Sun, Yu-Chi; Church, George M et al. (2018) Efficient in situ barcode sequencing using padlock probe-based BaristaSeq. Nucleic Acids Res 46:e22
Lee, Je H (2018) Tracing single-cell histories. Science 359:521-522
Lee, Je H (2017) De Novo Gene Expression Reconstruction in Space. Trends Mol Med 23:583-593
Lee, Je H (2017) Quantitative approaches for investigating the spatial context of gene expression. Wiley Interdiscip Rev Syst Biol Med 9: