Reprogramming, oscillations and transdifferentiation in epigenetic landscapes

Chaos in a bacterial stress response

Cellular responses to environmental changes are often highly heterogeneous and exhibit seemingly random dynamics. The astonishing insight of chaos theory is that such unpredictable patterns can, in principle, arise without the need for any random processes, i.e., purely deterministically without noise. However, while chaos is well understood in mathematics and physics, its role in cell biology remains unclear because the complexity and noisiness of biological systems make testing difficult. Here, we show that chaos explains the heterogeneous response of Escherichia coli cells to oxidative stress. We developed a theoretical model of the gene expression dynamics and demonstrate that chaotic behavior arises from rapid molecular feedbacks that are coupled with cell growth dynamics and cell-cell interactions. Based on theoretical predictions, we then designed single-cell experiments to show we can shift gene expression from periodic oscillations to chaos on demand. Our work suggests that chaotic gene regulation can be employed by cell populations to generate strong and variable responses to changing environments.

Morphogen-directed cell fate boundaries: slow passage through bifurcation and the role of folded saddles

One of the fundamental mechanisms in embryogenesis is the process by which cells differentiate and create tissues and structures important for functioning as a multicellular organism. Morphogenesis involves diffusive process of chemical signalling involving morphogens that pre-pattern the tissue. These morphogens influence cell fate through a highly nonlinear process of transcriptional signalling. In this paper, we consider this multiscale process in an idealised model for a growing domain. We focus on intracellular processes that lead to robust differentiation into two cell lineages through interaction of a single morphogen species with a cell fate variable that undergoes a bifurcation from monostability to bistability. In particular, we investigate conditions that result in successful and robust pattern formation into two well-separated domains, as well as conditions where this fails and produces a pinned boundary wave where only one part of the domain grows. We show that successful and unsuccessful patterning scenarios can be characterised in terms of presence or absence of a folded saddle singularity for a system with two slow variables and one fast variable; this models the interaction of slow morphogen diffusion, slow parameter drift through bifurcation and fast transcription dynamics. We illustrate how this approach can successfully model acquisition of three cell fates to produce three-domain "French flag" patterning, as well as for a more realistic model of the cell fate dynamics in terms of two mutually inhibiting transcription factors.

Determination of protoplast growth properties using quantitative single-cell tracking analysis

BACKGROUND

Although quantitative single-cell analysis is frequently applied in animal systems, e.g. to identify novel drugs, similar applications on plant single cells are largely missing. We have exploited the applicability of high-throughput microscopic image analysis on plant single cells using tobacco leaf protoplasts, cell-wall free single cells isolated by lytic digestion. Protoplasts regenerate their cell wall within several days after isolation and have the potential to expand and proliferate, generating microcalli and finally whole plants after the application of suitable regeneration conditions.

RESULTS

High-throughput automated microscopy coupled with the development of image processing pipelines allowed to quantify various developmental properties of thousands of protoplasts during the initial days following cultivation by immobilization in multi-well-plates. The focus on early protoplast responses allowed to study cell expansion prior to the initiation of proliferation and without the effects of shape-compromising cell walls. We compared growth parameters of wild-type tobacco cells with cells expressing the antiapoptotic protein Bcl2-associated athanogene 4 from Arabidopsis (AtBAG4).

CONCLUSIONS

AtBAG4-expressing protoplasts showed a higher proportion of cells responding with positive area increases than the wild type and showed increased growth rates as well as increased proliferation rates upon continued cultivation. These features are associated with reported observations on a BAG4-mediated increased resilience to various stress responses and improved cellular survival rates following transformation approaches. Moreover, our single-cell expansion results suggest a BAG4-mediated, cell-independent increase of potassium channel abundance which was hitherto reported for guard cells only. The possibility to explain plant phenotypes with single-cell properties, extracted with the single-cell processing and analysis pipeline developed, allows to envision novel biotechnological screening strategies able to determine improved plant properties via single-cell analysis.

Novel generic models for differentiating stem cells reveal oscillatory mechanisms

Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically motivated mathematical models for cell differentiation that generically generate oscillations and hence suggest alternatives to the standard framework based on Waddington's epigenetic landscape. The models allow us to suggest two generic dynamical scenarios that describe the differentiation process. In the first scenario, gradual variation of a single control parameter is responsible for both entering and exiting the oscillatory regime. In the second scenario, two control parameters vary: one responsible for entering, and the other for exiting the oscillatory regime. We analyse the standard repressilator and four variants of it and show the dynamical behaviours associated with each scenario. We present a thorough analysis of the associated bifurcations and argue that gene regulatory networks with these repressilator-like characteristics are promising candidates to describe cell fate selection through an oscillatory process.

Cellular Reprogramming and Immortality: Expression Profiling Reveals Putative Genes Involved in Turritopsis dohrnii's Life Cycle Reversal

To gather insight on the genetic network of cell reprogramming and reverse development in a nonmodel cnidarian system, we produced and annotated a transcriptome of the hydrozoan Turritopsis dohrnii, whose medusae respond to damage or senescence by metamorphosing into a juvenile stage (the polyp), briefly passing through an intermediate and uncharacterized stage (the cyst), where cellular transdifferentiation occurs. We conducted sequential and pairwise differential gene expression (DGE) analyses of the major life cycle stages involved in the ontogenetic reversal of T. dohrnii. Our DGE analyses of sequential stages of T. dohrnii's life cycle stages show that novel and characterized genes associated with aging/lifespan, regulation of transposable elements, DNA repair, and damage response, and Ubiquitin-related processes, among others, were enriched in the cyst stage. Our pairwise DGE analyses show that, when compared with the colonial polyp, the medusa is enriched with genes involved in membrane transport, the nervous system, components of the mesoglea, and muscle contraction, whereas genes involved in chitin metabolism and the formation of the primary germ layers are suppressed. The colonial polyp and reversed polyp (from cyst) show significant differences in gene expression. The reversed polyp is enriched with genes involved in processes such as chromatin remodeling and organization, matrix metalloproteinases, and embryonic development whereas suppressing genes involved in RAC G-protein signaling pathways. In summary, we identify genetic networks potentially involved in the reverse development of T. dohrnii and produce a transcriptome profile of all its life cycle stages, and paving the way for its use as a system for research on cell reprogramming.

Reconstructing an epigenetic landscape using a genetic pulling approach

Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an epigenetic landscape with phenotypic changes being transitions between states. Measuring these transitions is challenging because they are both very rare in the absence of appropriate signals and very fast. As such, it has proved difficult to experimentally map the epigenetic landscapes that are widely believed to underly developmental networks. Here, we introduce a nonequilibrium perturbation method to help reconstruct a regulatory network's epigenetic landscape. We derive the mathematical theory needed and then use the method on simulated data to reconstruct the landscapes. Our results show that with a relatively small number of perturbation experiments it is possible to recover an accurate representation of the true epigenetic landscape. We propose that our theory provides a general method by which epigenetic landscapes can be studied. Finally, our theory suggests that the total perturbation impulse required to induce a switch between metastable states is a fundamental quantity in developmental dynamics.

Operating principles of circular toggle polygons

Decoding the dynamics of cellular decision-making and cell differentiation is a central question in cell and developmental biology. A common network motif involved in many cell-fate decisions is a mutually inhibitory feedback loop between two self-activating 'master regulators' A and B, also called as toggle switch. Typically, it can allow for three stable states-(high A, low B), (low A, high B) and (medium A, medium B). A toggle triad-three mutually repressing regulators A, B and C, i.e. three toggle switches arranged circularly (between A and B, between B and C, and between A and C)-can allow for six stable states: three 'single positive' and three 'double positive' ones. However, the operating principles of larger toggle polygons, i.e. toggle switches arranged circularly to form a polygon, remain unclear. Here, we simulate using both discrete and continuous methods the dynamics of different sized toggle polygons. We observed a pattern in their steady state frequency depending on whether the polygon was an even or odd numbered one. The even-numbered toggle polygons result in two dominant states with consecutive components of the network expressing alternating high and low levels. The odd-numbered toggle polygons, on the other hand, enable more number of states, usually twice the number of components with the states that follow 'circular permutation' patterns in their composition. Incorporating self-activations preserved these trends while increasing the frequency of multistability in the corresponding network. Our results offer insights into design principles of circular arrangement of regulatory units involved in cell-fate decision making, and can offer design strategies for synthesizing genetic circuits.

Tunability enhancement of gene regulatory motifs through competition for regulatory protein resources

Gene regulatory networks (GRNs) orchestrate the spatiotemporal levels of gene expression, thereby regulating various cellular functions ranging from embryonic development to tissue homeostasis. Some patterns called "motifs" recurrently appear in the GRNs. Owing to the prevalence of these motifs they have been subjected to much investigation, both in the context of understanding cellular decision making and engineering synthetic circuits. Mounting experimental evidence suggests that (1) the copy number of genes associated with these motifs varies, and (2) proteins produced from these genes bind to decoy binding sites on the genome as well as promoters driving the expression of other genes. Together, these two processes engender competition for protein resources within a cell. To unravel how competition for protein resources affects the dynamical properties of regulatory motifs, we propose a simple kinetic model that explicitly incorporates copy number variation (CNV) of genes and decoy binding of proteins. Using quasi-steady-state approximations, we theoretically investigate the transient and steady-state properties of three of the commonly found motifs: Autoregulation, toggle switch, and repressilator. While protein resource competition alters the timescales to reach the steady state for all these motifs, the dynamical properties of the toggle switch and repressilator are affected in multiple ways. For toggle switch, the basins of attraction of the known attractors are dramatically altered if one set of proteins binds to decoys more frequently than the other, an effect which gets suppressed as the copy number of the toggle switch is enhanced. For repressilators, protein sharing leads to an emergence of oscillation in regions of parameter space that were previously nonoscillatory. Intriguingly, both the amplitude and frequency of oscillation are altered in a nonlinear manner through the interplay of CNV and decoy binding. Overall, competition for protein resources within a cell provides an additional layer of regulation of gene regulatory motifs.

Exploring the mechanisms of cell reprogramming and transdifferentiation via intercellular communication

In the past years, the mechanisms of cell reprogramming and transdifferentiation via the way of gene regulation, stochastic fluctuations, or chemical induction to realize cell type transitions from the perspectives of single cells were explored. In multicellular organisms, intercellular communication plays crucial roles in cell fate decisions. However, the importance of intercellular communication to the processes of cell reprogramming and transdifferentiation is often neglected. In this paper, the mechanisms of cell reprogramming and transdifferentiation by intercellular communication are investigated. A two-gene circuit with mutual inhibition and self-activation as a basic model is selected. Then, a coupling mechanism via intercellular communication by introducing a specific signaling molecule into the gene circuit is considered. Finally, the influence of coupling intensity on the dynamics of the coupled system of two cells is analyzed. Moreover, when the coupling intensity changes with respect to the cell number in a discrete way, the effects of coupling intensity on cell reprogramming and transdifferentiation are discussed. Some theoretical analysis of stability and bifurcation of the systems are also given. Our research shows that cells can realize cell reprogramming and transdifferentiation via intercellular interaction at opportune coupling intensity. These results not only further enrich previous studies but also are beneficial to understand the mechanisms of cell reprogramming and transdifferentiation via intercellular communication in the growth and development of multicellular organisms.