Tae Lee - Academia.edu (original) (raw)
Papers by Tae Lee
Nature Cell Biology, 2008
Nanotechnology in Biology and Medicine, 2007
Synthetic biology has emerged as a useful approach to decoding fundamental laws underlying biolog... more Synthetic biology has emerged as a useful approach to decoding fundamental laws underlying biological control. Recent efforts have produced many exciting systems and generated substantial insights. These progresses highlight the potential of synthetic biology to impact diverse areas including biology, computation, engineering, and medicine. 20.1 Introduction Biological systems often function reliably in diverse environments despite internal or external perturbations. This behavior is often characterized as ''robustness.'' Based on extensive studies over the last several decades, much of this robustness can be attributed to the control of gene expression through complex cellular networks [1-4]. These networks are known to consist of various regulatory modules, including feedback [5] and feed-forward [6] regulation and cell-cell communication [7]. With these basic regulatory modules and motifs, researchers are now constructing artificial networks that mimic nature to gain fundamental biological insight and understanding [8]. In addition, other artificial networks that are engineered with novel functions will serve as building blocks for future practical applications. These efforts form the foundation of the recent emergence of synthetic biology [3,9,10]. These artificial networks are interchangeably called ''synthetic gene circuits'' or ''engineered gene circuits.'' Recent accomplishments in synthetic biology include engineered switches [11-14], oscillators [15,16], logic gates [17-19], metabolic control [20], reengineered translational machinery [21], population control [22] and pattern formation [23] using natural or synthetic [24] cell-cell communication, reengineered viral genome [25], and hierarchically complex circuits built upon smaller, well-characterized
G3 (Bethesda, Md.), Jan 10, 2014
Recent studies have shown that proximal arrangement of multiple genes can have complex effects on... more Recent studies have shown that proximal arrangement of multiple genes can have complex effects on gene expression. For example, in the case of heterologous gene expression modules, certain arrangements of the selection marker and the gene expression cassette may have unintended consequences that limit the predictability and interpretability of module behaviors. The relationship between arrangement and expression has not been systematically characterized within heterologous modules to date. In this study, we quantitatively measured gene expression patterns of the selection marker (KlURA3 driven by the promoter, pKlURA) and the gene expression cassette (GFP driven by the galactose-inducible GAL1 promoter, pGAL1) in all their possible relative arrangements in Saccharomyces cerevisiae. First, we observed that pKlURA activity depends strongly on the relative arrangement and the activity of pGAL1. Most notably, we observed transcriptional suppression in the case of divergent arrangements:...
Cell reports, Jan 17, 2017
Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regene... more Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regenerative and can replace entire limbs. The mechanisms underlying limb regeneration remain poorly understood, partly because the enormous and incompletely sequenced genomes of axolotls have hindered the study of genes facilitating regeneration. We assembled and annotated a de novo transcriptome using RNA-sequencing profiles for a broad spectrum of tissues that is estimated to have near-complete sequence information for 88% of axolotl genes. We devised expression analyses that identified the axolotl orthologs of cirbp and kazald1 as highly expressed and enriched in blastemas. Using morpholino anti-sense oligonucleotides, we find evidence that cirbp plays a cytoprotective role during limb regeneration whereas manipulation of kazald1 expression disrupts regeneration. Our transcriptome and annotation resources greatly complement previous transcriptomic studies and will be a valuable resource fo...
PLoS computational biology, 2015
Pathogenic bacteria such as Listeria and Yersinia gain initial entry by binding to host target ce... more Pathogenic bacteria such as Listeria and Yersinia gain initial entry by binding to host target cells and stimulating their internalization. Bacterial uptake entails successive, increasingly strong associations between receptors on the surface of bacteria and hosts. Even with genetically identical cells grown in the same environment, there are vast differences in the number of bacteria entering any given cell. To gain insight into this variability, we examined uptake dynamics of Escherichia coli engineered to express the invasin surface receptor from Yersinia, which enables uptake via mammalian host β1-integrins. Surprisingly, we found that the uptake probability of a single bacterium follows a simple power-law dependence on the concentration of integrins. Furthermore, the value of a power-law parameter depends on the particular host-bacterium pair but not on bacterial concentration. This power-law captures the complex, variable processes underlying bacterial invasion while also enab...
Methods, 2013
We provide a guide to performing a sensitivity analysis (SA) of quantitative models of gene expre... more We provide a guide to performing a sensitivity analysis (SA) of quantitative models of gene expression dynamics appropriate to the levels of uncertainty in the model: spanning cases where parameters are relatively well-constrained to cases where they are poorly constrained. In the well-constrained case, we present methods to perform ''local'' SA (LSA), which considers small perturbations for a single set of model parameter values. In the poorly-constrained case, we present methods to perform ''global'' SA (GSA) as a means to evaluate the sensitivity of a model over large regions of parameter space. We apply these methods to quantitative models of increasing complexity. The models we consider are simple logistic growth, negative feedback in a mRNA-protein model, and two models of decision making within bacteriophage k. We discuss the best practices for how SA can be utilized in an iterative fashion to advance biological understanding.
PloS one, 2014
Many cellular decision processes, including proliferation, differentiation, and phenotypic switch... more Many cellular decision processes, including proliferation, differentiation, and phenotypic switching, are controlled by bistable signaling networks. In response to transient or intermediate input signals, these networks allocate a population fraction to each of two distinct states (e.g. OFF and ON). While extensive studies have been carried out to analyze various bistable networks, they are primarily focused on responses of bistable networks to sustained input signals. In this work, we investigate the response characteristics of bistable networks to transient signals, using both theoretical analysis and numerical simulation. We find that bistable systems exhibit a common property: for input signals with short durations, the fraction of switching cells increases linearly with the signal duration, allowing the population to integrate transient signals to tune its response. We propose that this allocation algorithm can be an optimal response strategy for certain cellular decisions in w...
The transition of the mammalian cell from quiescence to proliferation is a highly variable proces... more The transition of the mammalian cell from quiescence to proliferation is a highly variable process. Over the last four decades, two lines of apparently contradictory, phenomenological models have been proposed to account for such temporal variability. These include various forms of the transition probability (TP) model and the growth control (GC) model, which lack mechanistic details. The GC model was further proposed as an alternative explanation for the concept of the restriction point, which we recently demonstrated as being controlled by a bistable Rb-E2F switch. Here, through a combination of modeling and experiments, we show that these different lines of models in essence reflect different aspects of stochastic dynamics in cell cycle entry. In particular, we show that the variable activation of E2F can be described by stochastic activation of the bistable Rb-E2F switch, which in turn may account for the temporal variability in cell cycle entry. Moreover, we show that temporal dynamics of E2F activation can be recast into the frameworks of both the TP model and the GC model via parameter mapping. This mapping suggests that the two lines of phenomenological models can be reconciled through the stochastic dynamics of the Rb-E2F switch. It also suggests a potential utility of the TP or GC models in defining concise, quantitative phenotypes of cell physiology. This may have implications in classifying cell types or states.
The transcription factor Myc plays a central role in regulating cell-fate decisions, including pr... more The transcription factor Myc plays a central role in regulating cell-fate decisions, including proliferation, growth, and apoptosis. To maintain a normal cell physiology, it is critical that the control of Myc dynamics is precisely orchestrated. Recent studies suggest that such control of Myc can be achieved at the post-translational level via protein stability modulation. Myc is regulated by two Ras effector pathways: the extracellular signal-regulated kinase (Erk) and phosphatidylinositol 3-kinase (PI3K) pathways. To gain quantitative insight into Myc dynamics, we have developed a mathematical model to analyze post-translational regulation of Myc via sequential phosphorylation by Erk and PI3K. Our results suggest that Myc integrates Erk and PI3K signals to result in various cellular responses by differential stability control of Myc protein isoforms. Such signal integration confers a flexible dynamic range for the system output, governed by stability change. In addition, signal integration may require saturation of the input signals, leading to sensitive signal integration to the temporal features of the input signals, insensitive response to their amplitudes, and resistance to input fluctuations. We further propose that these characteristics of the protein stability control module in Myc may be commonly utilized in various cell types and classes of proteins.
In heterologous gene expression, a module with two gene circuits responsible for expression of a ... more In heterologous gene expression, a module with two gene circuits responsible for expression of a foreign gene of interest and selection is integrated into the host cell genome. Although the expression level of the foreign gene is generally understood to be determined by the strength of the promoter immediately upstream, several studies have shown that it varies significantly depending on the site and orientation of genomic integration. In addition, the arrangement of the selection circuit within the module may also affect the gene expression level. To test this possibility, we built a set of heterologous modules where two different gene circuits are placed right next to each other in all possible relative orientations. The activities of these gene circuits can be separately driven by external inducers and simultaneously monitored from fluorescent protein levels. We integrated these modules into the genome of budding yeast and quantitatively measured expression levels of both gene circuits at multiple inducer-level combinations. Our preliminary results show that the adjacent gene circuits interact in a cooperative and reciprocal manner; activation of the first gene circuit enhances the expression level of the second gene circuit and vice versa. Moreover, the degree of enhancement depends on the relative orientation of the gene circuits, highest when the promoters are pointing away from each other. Based on our results, we present a rate-equation based model to highlight potential mechanisms of promoter interaction.
Nature Cell Biology, 2008
Nanotechnology in Biology and Medicine, 2007
Synthetic biology has emerged as a useful approach to decoding fundamental laws underlying biolog... more Synthetic biology has emerged as a useful approach to decoding fundamental laws underlying biological control. Recent efforts have produced many exciting systems and generated substantial insights. These progresses highlight the potential of synthetic biology to impact diverse areas including biology, computation, engineering, and medicine. 20.1 Introduction Biological systems often function reliably in diverse environments despite internal or external perturbations. This behavior is often characterized as ''robustness.'' Based on extensive studies over the last several decades, much of this robustness can be attributed to the control of gene expression through complex cellular networks [1-4]. These networks are known to consist of various regulatory modules, including feedback [5] and feed-forward [6] regulation and cell-cell communication [7]. With these basic regulatory modules and motifs, researchers are now constructing artificial networks that mimic nature to gain fundamental biological insight and understanding [8]. In addition, other artificial networks that are engineered with novel functions will serve as building blocks for future practical applications. These efforts form the foundation of the recent emergence of synthetic biology [3,9,10]. These artificial networks are interchangeably called ''synthetic gene circuits'' or ''engineered gene circuits.'' Recent accomplishments in synthetic biology include engineered switches [11-14], oscillators [15,16], logic gates [17-19], metabolic control [20], reengineered translational machinery [21], population control [22] and pattern formation [23] using natural or synthetic [24] cell-cell communication, reengineered viral genome [25], and hierarchically complex circuits built upon smaller, well-characterized
G3 (Bethesda, Md.), Jan 10, 2014
Recent studies have shown that proximal arrangement of multiple genes can have complex effects on... more Recent studies have shown that proximal arrangement of multiple genes can have complex effects on gene expression. For example, in the case of heterologous gene expression modules, certain arrangements of the selection marker and the gene expression cassette may have unintended consequences that limit the predictability and interpretability of module behaviors. The relationship between arrangement and expression has not been systematically characterized within heterologous modules to date. In this study, we quantitatively measured gene expression patterns of the selection marker (KlURA3 driven by the promoter, pKlURA) and the gene expression cassette (GFP driven by the galactose-inducible GAL1 promoter, pGAL1) in all their possible relative arrangements in Saccharomyces cerevisiae. First, we observed that pKlURA activity depends strongly on the relative arrangement and the activity of pGAL1. Most notably, we observed transcriptional suppression in the case of divergent arrangements:...
Cell reports, Jan 17, 2017
Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regene... more Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regenerative and can replace entire limbs. The mechanisms underlying limb regeneration remain poorly understood, partly because the enormous and incompletely sequenced genomes of axolotls have hindered the study of genes facilitating regeneration. We assembled and annotated a de novo transcriptome using RNA-sequencing profiles for a broad spectrum of tissues that is estimated to have near-complete sequence information for 88% of axolotl genes. We devised expression analyses that identified the axolotl orthologs of cirbp and kazald1 as highly expressed and enriched in blastemas. Using morpholino anti-sense oligonucleotides, we find evidence that cirbp plays a cytoprotective role during limb regeneration whereas manipulation of kazald1 expression disrupts regeneration. Our transcriptome and annotation resources greatly complement previous transcriptomic studies and will be a valuable resource fo...
PLoS computational biology, 2015
Pathogenic bacteria such as Listeria and Yersinia gain initial entry by binding to host target ce... more Pathogenic bacteria such as Listeria and Yersinia gain initial entry by binding to host target cells and stimulating their internalization. Bacterial uptake entails successive, increasingly strong associations between receptors on the surface of bacteria and hosts. Even with genetically identical cells grown in the same environment, there are vast differences in the number of bacteria entering any given cell. To gain insight into this variability, we examined uptake dynamics of Escherichia coli engineered to express the invasin surface receptor from Yersinia, which enables uptake via mammalian host β1-integrins. Surprisingly, we found that the uptake probability of a single bacterium follows a simple power-law dependence on the concentration of integrins. Furthermore, the value of a power-law parameter depends on the particular host-bacterium pair but not on bacterial concentration. This power-law captures the complex, variable processes underlying bacterial invasion while also enab...
Methods, 2013
We provide a guide to performing a sensitivity analysis (SA) of quantitative models of gene expre... more We provide a guide to performing a sensitivity analysis (SA) of quantitative models of gene expression dynamics appropriate to the levels of uncertainty in the model: spanning cases where parameters are relatively well-constrained to cases where they are poorly constrained. In the well-constrained case, we present methods to perform ''local'' SA (LSA), which considers small perturbations for a single set of model parameter values. In the poorly-constrained case, we present methods to perform ''global'' SA (GSA) as a means to evaluate the sensitivity of a model over large regions of parameter space. We apply these methods to quantitative models of increasing complexity. The models we consider are simple logistic growth, negative feedback in a mRNA-protein model, and two models of decision making within bacteriophage k. We discuss the best practices for how SA can be utilized in an iterative fashion to advance biological understanding.
PloS one, 2014
Many cellular decision processes, including proliferation, differentiation, and phenotypic switch... more Many cellular decision processes, including proliferation, differentiation, and phenotypic switching, are controlled by bistable signaling networks. In response to transient or intermediate input signals, these networks allocate a population fraction to each of two distinct states (e.g. OFF and ON). While extensive studies have been carried out to analyze various bistable networks, they are primarily focused on responses of bistable networks to sustained input signals. In this work, we investigate the response characteristics of bistable networks to transient signals, using both theoretical analysis and numerical simulation. We find that bistable systems exhibit a common property: for input signals with short durations, the fraction of switching cells increases linearly with the signal duration, allowing the population to integrate transient signals to tune its response. We propose that this allocation algorithm can be an optimal response strategy for certain cellular decisions in w...
The transition of the mammalian cell from quiescence to proliferation is a highly variable proces... more The transition of the mammalian cell from quiescence to proliferation is a highly variable process. Over the last four decades, two lines of apparently contradictory, phenomenological models have been proposed to account for such temporal variability. These include various forms of the transition probability (TP) model and the growth control (GC) model, which lack mechanistic details. The GC model was further proposed as an alternative explanation for the concept of the restriction point, which we recently demonstrated as being controlled by a bistable Rb-E2F switch. Here, through a combination of modeling and experiments, we show that these different lines of models in essence reflect different aspects of stochastic dynamics in cell cycle entry. In particular, we show that the variable activation of E2F can be described by stochastic activation of the bistable Rb-E2F switch, which in turn may account for the temporal variability in cell cycle entry. Moreover, we show that temporal dynamics of E2F activation can be recast into the frameworks of both the TP model and the GC model via parameter mapping. This mapping suggests that the two lines of phenomenological models can be reconciled through the stochastic dynamics of the Rb-E2F switch. It also suggests a potential utility of the TP or GC models in defining concise, quantitative phenotypes of cell physiology. This may have implications in classifying cell types or states.
The transcription factor Myc plays a central role in regulating cell-fate decisions, including pr... more The transcription factor Myc plays a central role in regulating cell-fate decisions, including proliferation, growth, and apoptosis. To maintain a normal cell physiology, it is critical that the control of Myc dynamics is precisely orchestrated. Recent studies suggest that such control of Myc can be achieved at the post-translational level via protein stability modulation. Myc is regulated by two Ras effector pathways: the extracellular signal-regulated kinase (Erk) and phosphatidylinositol 3-kinase (PI3K) pathways. To gain quantitative insight into Myc dynamics, we have developed a mathematical model to analyze post-translational regulation of Myc via sequential phosphorylation by Erk and PI3K. Our results suggest that Myc integrates Erk and PI3K signals to result in various cellular responses by differential stability control of Myc protein isoforms. Such signal integration confers a flexible dynamic range for the system output, governed by stability change. In addition, signal integration may require saturation of the input signals, leading to sensitive signal integration to the temporal features of the input signals, insensitive response to their amplitudes, and resistance to input fluctuations. We further propose that these characteristics of the protein stability control module in Myc may be commonly utilized in various cell types and classes of proteins.
In heterologous gene expression, a module with two gene circuits responsible for expression of a ... more In heterologous gene expression, a module with two gene circuits responsible for expression of a foreign gene of interest and selection is integrated into the host cell genome. Although the expression level of the foreign gene is generally understood to be determined by the strength of the promoter immediately upstream, several studies have shown that it varies significantly depending on the site and orientation of genomic integration. In addition, the arrangement of the selection circuit within the module may also affect the gene expression level. To test this possibility, we built a set of heterologous modules where two different gene circuits are placed right next to each other in all possible relative orientations. The activities of these gene circuits can be separately driven by external inducers and simultaneously monitored from fluorescent protein levels. We integrated these modules into the genome of budding yeast and quantitatively measured expression levels of both gene circuits at multiple inducer-level combinations. Our preliminary results show that the adjacent gene circuits interact in a cooperative and reciprocal manner; activation of the first gene circuit enhances the expression level of the second gene circuit and vice versa. Moreover, the degree of enhancement depends on the relative orientation of the gene circuits, highest when the promoters are pointing away from each other. Based on our results, we present a rate-equation based model to highlight potential mechanisms of promoter interaction.