-From Images to Phenomes: Single-Cell Analysis of Embryogenesis

Embryogenesis is a complex process during which the genome creates an organism. Recent progresses in reverse genetics, live imaging and image bioinformatics have opened the door for a systems-level functional dissection of embryogenesis in a high-throughput, high-resolution, in-depth and quantitative manner.  We are applying an automated phenotyping system to quantify developmental phenotypes of individual embryonic cells. It relies on long-term 3D, time-lapse imaging of C. elegans embryogenesis followed by transformation of 4D images into quantitative measurements of single cell's developmental behaviors in terms of gene expression, proliferation, differentiation and morphogenesis (Development, 2013). This system allows acquisition and processing of ~ 5,000 embryos per microscope each year. We are applying this versatile system to perform genome-scale perturbations and high-dimensional phenotypic analysis of embryogenesis. Our goal is to decode how genome and genetic networks instruct the dynamic behavior and function of every cell during every minute of development.

-From Phenotypes to Regulation: Cell Fate Choice

Elucidating genes and regulatory networks that drive series of cell fate choices during cell differentiation is a fundamental question for developmental biology and cell engineering. How to define and assay developmental fate of progenitor cells in vivo is a major challenge towards systems biology of cell differentiation. We have developed a strategy to define progenitor cell fate by determining the cell lineage and combination of cell types a cell give rise to following development. Based on fate change phenotypes, we have devised an automated reasoning strategy to transform massive phenomics data into succinct mechanistic models of cell fate regulation. These develops provide a unique opportunity to detect cell fate changes and homeotic transformations following genetic perturbations to identify master regulators controlling cell fate determination in specific cells. In a proof-of-concept study we re-examined cell fate phenotypes for 20 extensively studied C. elegans developmental regulators and successfully recapitulated most of the known functions of these genes. Automated analysis also reveals many new regulatory processes and new gene functions such as a binary switch between self-renewal and differentiation in the endomesoderm progenitor cell. Through data integration we reconstructed a systems-wide mechanistic model on how gene modules and cell-to-cell signaling events regulate series of cell fate choices in the early embryos.  This study provides a powerful approach to investigate in vivo regulation of cell fate (Cell, 2014; Dev Biol. 2015). We are applying this method to investigate how chromatin factors, mediators and transcription factors regulate the specification, transition and differentiation of cell fates.

-From Genes to Genome: The Regulatory Landscape of Cell Lineage Differentiation

Regulation of cell lineage differentiation is a central question in developmental biology concerns the generation of all types of cells from a totipotent zygote. Using above approaches, we perturbed the essential genome and mapped the phenome of cell lineage differentiation in early C. elegans embryogenesis. We performed RNAi for hundreds of conserved essential genes and assayed differentiation of individual cells in ~1,400 embryos with a lethal phenotype. Using the phenotypes we achieved a large-scale annotation of gene function in lineage differentiation including 820 cellular functions for 201 genes in lineage differentiation and 175 regulatory switches of binary cell fate choice. We also revealed some general properties of the regulation of lineage differentiation. Integrated analysis of the phenotypes reveals a systemic canalization of cell fates in which the developmental landscape of lineage differentiation is canalized toward a small number of stable fates and lineage distance and genetic robustness determine the barriers between fates. This finding provides a systematic experimental evidence of canalization phenomenon and characterization of the properties of the developmental landscape. Lastly, to understand the regulatory network of lineage differentiation we constructed a multiscale model of lineage differentiation that connects gene networks and cells to the experimentally mapped landscape. At the systems level, simulations based on the model suggest that the topology of the landscape affects the propensity of differentiation and the minimal requirements for active regulation of fate choice. At the molecular level, the cellular resolution of the model revealed the chromatin assembly complex CAF-1 as a context-specific repressor of Notch signaling. Together, through systematic phenotypic analysis of lineage differentiation over time, space, and genome our study presents a systematic survey of the regulatory landscape of lineage differentiation of a metazoan embryo (Dev Cell, 2015; Nucleic Acids Res. 2016). On the basis of the multiscale model we are investigating how multigenic effects and genetic interactions regulate lineage differentiation.

-From Expression to Function: Spatiotemporal Regulatory Circuits of Transcription Factors

With the progresses in image bioinformatics and single-cell genomics it's feasible to map gene expression and transcriptome of single cells during development. While gene expression specifies functions, the next challenge is how to systematically transform cellular gene expression patterns to mechanistic understanding of developmental regulation. One efficient way to dissect function is to map the genetic and regulatory relationship between expressed genes in single cells. Transcription factor is an important gene category shaping the transcriptome hence function of a cell. We are taking live imaging, phenomics, and systems genetics approaches to map cellular genetic and regulatory circuits of conserved transcription factors in the C. elegans early embryos.  Our goal is to reveal how the molecular circuits form spatiotemporally in cells to regulate embryogenesis.

-From Genetics to Environment: Environmental Regulation of Embryogenesis

Misregulation of embryogenesis causes birth defects and developmental diseases.  While genetic determinants of embryogenesis has been subjected to extensively studies the effects of environmental factors, while widely recognized, are still poorly understood. We are using C. elegans embryogenesis to model developmental gene-environment interaction. To this end, we are applying chemical genetics and high-resolution phenotyping approaches to investigate how naturally occurring environmental factors (ecological factors, environmental hormones, chemicals and nutrient molecules) interact with in vivo genetic regulatory networks to regulate the robustness of embryogenesis.

-From Worms to Humans: C. elegans Models of Human Health and Diseases

The short life cycle and genetic tractability make C. elegans a versatile model organism to study many complex and important phenotypes/traits. We are interested in developing new C. elegans models to study reproduction, development, and growth associated processes relevant to human health and diseases.

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