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Register a new userFunctional models for large-scale gene regulation networks: realism and fiction
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High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different conditions, times, environments. We now possess a certain amount of information about these two levels of description, stored in libraries, databases and ontologies. A current challenge is to bridge the gap between topology and function, i.e. developing quantitative models aimed at characterizing the expression patterns of large sets of genes. However, approaches that work well for small networks become impossible to master at large scales, mainly because parameters proliferate. In this review we discuss the state of the art of large-scale functional network models, addressing the issue of what can be considered as realistic and what the main limitations may be. We also show some directions for future work, trying to set the goals that future models should try to achieve. Finally, we will emphasize the possible benefits in the understanding of biological mechanisms underlying complex multifactorial diseases, and in the development of novel strategies for the description and the treatment of such pathologies.
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Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data obtained from single-cell sequencing or flow-cytometry experiments into regulatory dynamics. We show how static population snapshots of co-variability can be exploited to rigorously infer properties of gene expression dynamics when gene expression reporters probe their upstream dynamics on separate time-scales. This can be experimentally exploited in dual-reporter experiments with fluorescent proteins of unequal maturation times, thus turning an experimental bug into an analysis feature. We derive correlation conditions that detect the presence of closed-loop feedback regulation in gene regulatory networks. Furthermore, we show how genes with cell-cycle dependent transcription rates can be identified from the variability of co-regulated fluorescent proteins. Similar correlation constraints might prove useful in other areas of science in which static correlation snapshots are used to infer causal connections between dynamically interacting components.
We present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct accumulation. We provide a method to determine the steady states of this system that is tractable for metabolic networks of arbitrary complexity. We demonstrate our approach in a toy model first, and then in a genome-scale metabolic network of the Chinese hamster ovary cell line, obtaining results that are in qualitative agreement with experimental observations. More importantly, we derive a number of consequences from the model that are independent of parameter values. First, that the ratio between cell density and dilution rate is an ideal control parameter to fix a steady state with desired metabolic properties invariant across perfusion systems. This conclusion is robust even in the presence of multi-stability, which is explained in our model by the negative feedback loop on cell growth due to toxic byproduct accumulation. Moreover, a complex landscape of steady states in continuous cell culture emerges from our simulations, including multiple metabolic switches, which also explain why cell-line and media benchmarks carried out in batch culture cannot be extrapolated to perfusion. On the other hand, we predict invariance laws between continuous cell cultures with different parameters. A practical consequence is that the chemostat is an ideal experimental model for large-scale high-density perfusion cultures, where the complex landscape of metabolic transitions is faithfully reproduced. Thus, in order to actually reflect the expected behavior in perfusion, performance benchmarks of cell-lines and culture media should be carried out in a chemostat.
Complex biological functions are carried out by the interaction of genes and proteins. Uncovering the gene regulation network behind a function is one of the central themes in biology. Typically, it involves extensive experiments of genetics, biochemistry and molecular biology. In this paper, we show that much of the inference task can be accomplished by a deep neural network (DNN), a form of machine learning or artificial intelligence. Specifically, the DNN learns from the dynamics of the gene expression. The learnt DNN behaves like an accurate simulator of the system, on which one can perform in-silico experiments to reveal the underlying gene network. We demonstrate the method with two examples: biochemical adaptation and the gap-gene patterning in fruit fly embryogenesis. In the first example, the DNN can successfully find the two basic network motifs for adaptation - the negative feedback and the incoherent feed-forward. In the second and much more complex example, the DNN can accurately predict behaviors of essentially all the mutants. Furthermore, the regulation network it uncovers is strikingly similar to the one inferred from experiments. In doing so, we develop methods for deciphering the gene regulation network hidden in the DNN black box. Our interpretable DNN approach should have broad applications in genotype-phenotype mapping.
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF. However, molecular mechanisms underlying this folding, and the way folding affects transcriptional activity, remain obscure. Here we review physical principles driving proteins bound to long polymers into clusters surrounded by loops, and present a parsimonious yet comprehensive model for the way the organization determines function. We argue that clusters of active RNA polymerases and their transcription factors are major architectural features; then, contact domains, TADs, and compartments just reflect one or more loops and clusters. We suggest tethering a gene close to a cluster containing appropriate factors -- a transcription factory -- increases the firing frequency, and offer solutions to many current puzzles concerning the actions of enhancers, super-enhancers, boundaries, and eQTLs (expression quantitative trait loci). As a result, the activity of any gene is directly influenced by the activity of other transcription units around it in 3D space, and this is supported by Brownian-dynamics simulations of transcription factors binding to cognate sites on long polymers.
Magombedze and Mulder in 2013 studied the gene regulatory system of Mycobacterium Tuberculosis (Mtb) by partitioning this into three subsystems based on putative gene function and role in dormancy/latency development. Each subsystem, in the form of S-system, is represented by an embedded chemical reaction network (CRN), defined by a species subset and a reaction subset induced by the set of digraph vertices of the subsystem. For the embedded networks of S-system, we showed interesting structural properties and proved that all S-system CRNs (with at least two species) are discordant. Analyzing the subsystems as subnetworks, where arcs between vertices belonging to different subsystems are retained, we formed a digraph homomorphism from the corresponding subnetworks to the embedded networks. Lastly, we explored the modularity concept of CRN in the context of digraph.
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