Jana Wolf

Global quantification of mammalian gene expression control

Gene expression is a multistep process that involves the transcription, translation and turnover of messenger RNAs and proteins. Although it is one of the most fundamental processes of life, the entire cascade has never been quantified on a genome-wide scale. Here we simultaneously measured absolute mRNA and protein abundance and turnover by parallel metabolic pulse labelling for more than 5,000 genes in mammalian cells. Whereas mRNA and protein levels correlated better than previously thought, corresponding half-lives showed no correlation. Using a quantitative model we have obtained the first genome-scale prediction of synthesis rates of mRNAs and proteins. We find that the cellular abundance of proteins is predominantly controlled at the level of translation. Genes with similar combinations of mRNA and protein stability shared functional properties, indicating that half-lives evolved under energetic and dynamic constraints. Quantitative information about all stages of gene expression provides a rich resource and helps to provide a greater understanding of the underlying design principles.

Transduction of Intracellular and Intercellular Dynamics in Yeast Glycolytic Oscillations

Under certain well-defined conditions, a population of yeast cells exhibits glycolytic oscillations that synchronize through intercellular acetaldehyde. This implies that the dynamic phenomenon of the oscillation propagates within and between cells. We here develop a method to establish by which route dynamics propagate through a biological reaction network. Application of the method to yeast demonstrates how the oscillations and the synchronization signal can be transduced. That transduction is not so much through the backbone of glycolysis, as via the Gibbs energy and redox coenzyme couples (ATP/ADP, and NADH/NAD), and via both intra- and intercellular acetaldehyde.

Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation

On the basis of a detailed model of yeast glycolysis, the effect of intercellular dynamics is analysed theoretically. The model includes the main steps of anaerobic glycolysis, and the production of ethanol and glycerol. Transmembrane diffusion of acetaldehyde is included, since it has been hypothesized that this substance mediates the interaction. Depending on the kinetic parameter, the single-cell model shows both stationary and oscillatory behaviour. This agrees with experimental data with respect to metabolite concentrations and phase shifts. The inclusion of intercellular coupling leads to a variety of dynamical modes, such as synchronous oscillations, and different kinds of asynchronous behavior. These oscillations can co-exist, leading to bi- and tri-rhythmicity. The corresponding parameter regions have been identified by a bifurcation analysis. The oscillatory dynamics of synchronized cell populations are investigated by calculating the phase responses to acetaldehyde pulses. Simulations are performed with respect to the synchronization of two subpopulations that are oscillating out of phase before mixing. The effect of the various process on synchronization is characterized quantitatively. While continuous exchange of acetaldehyde might synchronize the oscillations for appropriate sets of parameter values, the calculated synchronization time is longer than that observed experimentally. It is concluded either that addition to the transmembrane exchange of acetaldehyde, other processes may contribute to intercellular coupling, or that intracellular regulator feedback plays a role in the acceleration of the synchronization. for appropriate sets of parameter values, the calculated synchronization time is longer than that observed experimentally. It is concluded either that addition to the transmembrane exchange of acetaldehyde, other processes may contribute to intercellular coupling, or that intracellular regulator feedback plays a role in the acceleration of the synchronization.

Corrigendum: Global quantification of mammalian gene expression control

This corrects the article DOI: 10.1038/nature10098

Quantitative modelling of amyloidogenic processing and its influence by SORLA in Alzheimer's disease

The extent of proteolytic processing of the amyloid precursor protein (APP) into neurotoxic amyloid‐β (Aβ) peptides is central to the pathology of Alzheimers disease (AD). Accordingly, modifiers that increase Aβ production rates are risk factors in the sporadic form of AD. In a novel systems biology approach, we combined quantitative biochemical studies with mathematical modelling to establish a kinetic model of amyloidogenic processing, and to evaluate the influence by SORLA/SORL1, an inhibitor of APP processing and important genetic risk factor. Contrary to previous hypotheses, our studies demonstrate that secretases represent allosteric enzymes that require cooperativity by APP oligomerization for efficient processing. Cooperativity enables swift adaptive changes in secretase activity with even small alterations in APP concentration. We also show that SORLA prevents APP oligomerization both in cultured cells and in the brain in vivo, eliminating the preferred form of the substrate and causing secretases to switch to a less efficient non‐allosteric mode of action. These data represent the first mathematical description of the contribution of genetic risk factors to AD substantiating the relevance of subtle changes in SORLA levels for amyloidogenic processing as proposed for patients carrying SORL1 risk alleles.

DYNAMICS OF TWO-COMPONENT BIOCHEMICAL SYSTEMS IN INTERACTING CELLS ; SYNCHRONIZATION AND DESYNCHRONIZATION OF OSCILLATIONS AND MULTIPLE STEADY STATES

Systems of interacting cells containing a metabolic pathway with an autocatalytic reaction are investigated. The individual cells are considered to be identical and are described by differential equations proposed for the description of glycolytic oscillations. The coupling is realized by exchange of metabolites across the cell membranes. No constraints are introduced concerning the number of interacting systems, that is, the analysis applies also to populations with a high number of cells. Two versions of the model are considered where either the product or the substrate of the autocatalytic reaction represents the coupling metabolite (Model I and II, respectively). Model I exhibits a unique steady state while model II shows multistationary behaviour where the number of steady states increases strongly with the number of cells. The characteristic polynomials used for a local stability analysis are factorized into polynomials of lower degrees. From the various factors different Hopf bifurcations may result in leading for model I, either to asynchronous oscillations with regular phase shifts or to synchronous oscillations of the cells depending on the strength of the coupling and on the cell density. The multitude of steady states obtained for model II may be grouped into one class of states which are always unstable and another class of states which may undergo bifurcations leading to synchronous oscillations within subgroups of cells. From these bifurcations numerous different oscillatory regimes may emerge. Leaving the near neighbourhood of the boundary of stability, secondary bifurcations of the limit cycles occur in both models. By symmetry breaking the resulting oscillations for the individual cells lose their regular phase shifts. These complex dynamic phenomena are studied in more detail for a low number of interacting cells. The theoretical results are discussed in the light of recent experimental data on the synchronization of oscillations in populations of yeast cells.

Temperature dependency and temperature compensation in a model of yeast glycolytic oscillations

Temperature sensitivities and conditions for temperature compensation have been investigated in a model for yeast glycolytic oscillations. The model can quantitatively simulate the experimental observation that the period length of glycolytic oscillations decreases with increasing temperature. Temperature compensation is studied by using control coefficients describing the effect of rate constants on oscillatory frequencies. Temperature compensation of the oscillatory period is observed when the positive contributions to the sum of products between control coefficients and activation energies balance the corresponding sum of the negative contributions. The calculations suggest that by changing the activation energies for one or several of the processes, i.e. by mutations, it could be possible to obtain temperature compensation in the yeast glycolytic oscillator.

Different promoter affinities account for specificity in MYC-dependent gene regulation

Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. We determined cellular MYC levels and used RNA- and ChIP-sequencing to correlate promoter occupancy with gene expression at different concentrations of MYC. Mathematical modeling showed that binding affinities for interactions of MYC with DNA and with core promoter-bound factors, such as WDR5, are sufficient to explain promoter occupancies observed in vivo. Importantly, promoter affinity stratifies different biological processes that are regulated by MYC, explaining why tumor-specific MYC levels induce specific gene expression programs and alter defined biological properties of cells. DOI: http://dx.doi.org/10.7554/eLife.15161.001

RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.

The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNFα mRNA decay via a 3′UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ∼3,800 mRNA targets with >16,000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins. RC3H1 binds preferentially short-lived and DNA damage-induced mRNAs, indicating a role of this RNA-binding protein in the post-transcriptional regulation of the DNA damage response. Intriguingly, RC3H1 affects expression of the NF-κB pathway regulators such as IκBα and A20. RC3H1 uses ROQ and Zn-finger domains to contact a binding site in the A20 3′UTR, demonstrating a not yet recognized mode of RC3H1 binding. Knockdown of RC3H1 resulted in increased A20 protein expression, thereby interfering with IκB kinase and NF-κB activities, demonstrating that RC3H1 can modulate the activity of the IKK/NF-κB pathway.

Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisiae

Autonomous metabolic oscillations were observed in aerobic continuous culture of Saccharomyces cerevisiae. Experimental investigation of the underlying mechanism revealed that several pathways and regulatory couplings are involved. Here a hypothetical mechanism including the sulfate assimilation pathway, ethanol degradation and respiration is transformed into a mathematical model. Simulations confirm the ability of the model to produce limit cycle oscillations which reproduce most of the characteristic features of the system.