Symmetry-breaking phase transition in a dynamical decision model

We consider a simple decision model in which a set of agents randomly choose one of two competing shops selling the same perishable products (typically food). The satisfaction of agents with respect to a given store is related to the freshness of the previously bought products. Agents select with a higher probability the store they are most satisfied with. Studying the model from a statistical physics perspective, both through numerical simulations and mean-field analytical methods, we find a rich behaviour with continuous and discontinuous phase transitions between a symmetric phase where both stores maintain the same level of activity, and a phase with broken symmetry where one of the two shops attracts more customers than the other.Comment: 13 pages, 6 figures, submitted to JSTA

Systematic discovery of drug interaction mechanisms

Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways

Quantifying the determinants of evolutionary dynamics leading to drug resistance

The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution

Open chromatin encoded in DNA sequence is the signature of ‘master’ replication origins in human cells

For years, progress in elucidating the mechanisms underlying replication initiation and its coupling to transcriptional activities and to local chromatin structure has been hampered by the small number (approximately 30) of well-established origins in the human genome and more generally in mammalian genomes. Recent in silico studies of compositional strand asymmetries revealed a high level of organization of human genes around 1000 putative replication origins. Here, by comparing with recently experimentally identified replication origins, we provide further support that these putative origins are active in vivo. We show that regions ∼300-kb wide surrounding most of these putative replication origins that replicate early in the S phase are hypersensitive to DNase I cleavage, hypomethylated and present a significant enrichment in genomic energy barriers that impair nucleosome formation (nucleosome-free regions). This suggests that these putative replication origins are specified by an open chromatin structure favored by the DNA sequence. We discuss how this distinctive attribute makes these origins, further qualified as ‘master’ replication origins, priviledged loci for future research to decipher the human spatio-temporal replication program. Finally, we argue that these ‘master’ origins are likely to play a key role in genome dynamics during evolution and in pathological situations

Influence of the genomic sequence on the primary structure of chromatin

International audienceAs an important actor in the regulation of nuclear functions, the nucleosomal organization of the 10 nm chromatin fiber is the subject of increasing interest. Recent high-resolution mapping of nucleosomes along various genomes ranging from yeast to human, have revealed a patchy nucleosome landscape with alternation of depleted, well positioned and fuzzy regions. For many years, the mechanisms that control nucleosome occupancy along eukaryotic chromosomes and their coupling to transcription and replication processes have been under intense experimental and theoretical investigation. A recurrent question is to what extent the genomic sequence dictates and/or constrains nucleosome positioning and dynamics? In that context we have recently developed a simple thermodynamical model that accounts for both sequence specificity of the histone octamer and for nucleosome–nucleosome interactions. As a main issue, our modelling mimics remarkably well in vitro data showing that the sequence signaling that prevails are high energy barriers that locally inhibit nucleosome formation and condition the collective positioning of neighboring nucleosomes according to thermal equilibrium statistical ordering. When comparing to in vivo data, our physical modelling performs as well as models based on statistical learning suggesting that in vivo bulk chromatin is to a large extent controlled by the underlying genomic sequence although it is also subject to finite-range remodelling action of external factors including transcription factors and ATP-dependent chromatin remodellers. On the highly studied S. cerevisiae organism, we discuss the implications of the highlighted ‘positioning via excluding’ mechanism on the structure and function of yeast genes. The generalization of our physical modelling to human is likely to provide new insight on the isochore structure of mammalian genomes in relation with their primary nucleosomal structure

Thermodynamique du positionnement des nucléosomes

Le nucléosome est un complexe de protéines qui autorise une meilleure organisation de l'ADN au sein du noyau. L'affinité du nucléosome pour l'ADN varie en fonction de la séquence ce qui altère certains mécanismes biologiques comme la régulation ou l'expression des gènes. La description du chapelet nucléosomal comme un fluide 1D de tiges rigides permet des prédictions excellentes sur les données de reconstitution (in vitro) de nucléosomes. Les différences observées avec le chapelet réel sont interprétées par l'action de facteurs extérieurs au nombre desquels on peut compter : les facteurs de transcription, le remodelage et les chaperonnes. Deux aspects apparaissent essentiels : le positionnement intrinsèque dû à la séquence et le positionnement statistique issu de l'interaction des nucléosomes avec des obstacles. Les conséquences biologiques sont notables : la forme de la chromatine à l'intérieur des gènes et au niveau du promoteur influence la régulation de l'expression.The nucleosome is a eukaryotic protein complex whose main role is to organise the DNA inside the nucleus. The affinity of the DNA for the nucleosome depends on the sequence so that essential biological mechanisms such as gene regulation and expression are affected. Modeling the nucleosomal array as a 1D fluid of hard rods yields excellent predictions for in vitro reconstitution data. The discrepencies observed in vivo are interpreted by the action of external factors such as remodellers, transcription factors and haperones. We investigate the intrinsic positioning induced by the sequence as well as the statistical positioning induced by nucleosomes interaction with boundary elements in the energetic profile in which they are set. The nucleosomal array induced by these elements had some biological consequences since the chromatin conformation inside genes and at the promoter influences gene expression.LYON-ENS Sciences (693872304) / SudocSudocFranceF

Thermodynamics of Intragenic Nucleosome Ordering

The nucleosome ordering observed in vivo along yeast genes is described by a thermodynamical model of nonuniform fluid of 1D hard rods confined by two excluding energy barriers at gene extremities. For interbarrier distances L≲1.5  kbp, nucleosomes equilibrate into a crystal-like configuration with a nucleosome repeat length (NRL) L/n∼165  bp, where n is the number of regularly positioned nucleosomes. We also observe “bistable” genes with a fuzzy chromatin resulting from a statistical mixing of two crystal states, one with an expanded chromatin (NRL ∼L/n) and the other with a compact one (NRL ∼L/(n+1)). By means of single nucleosome switching, bistable genes may drastically alter their expression level as suggested by their higher transcriptional plasticity. These results enlighten the role of the intragenic chromatin on gene expression regulation

Symmetry-breaking phase transition in a dynamical decision model

13 pages, 6 figures, submitted to JSTATInternational audienceWe consider a simple decision model in which a set of agents randomly choose one of two competing shops selling the same perishable products (typically food). The satisfaction of agents with respect to a given store is related to the freshness of the previously bought products. Agents select with a higher probability the store they are most satisfied with. Studying the model from a statistical physics perspective, both through numerical simulations and mean-field analytical methods, we find a rich behaviour with continuous and discontinuous phase transitions between a symmetric phase where both stores maintain the same level of activity, and a phase with broken symmetry where one of the two shops attracts more customers than the other

A novel strategy of transcription regulation by intragenic nucleosome ordering.

Numerous studies of chromatin structure showed that nucleosome free regions (NFRs) located at 5' gene ends contribute to transcription initiation regulation. Here, we determine the role of intragenic chromatin structure on gene expression regulation. We show that, along Saccharomyces cerevisiae genes, nucleosomes are highly organized following two types of architecture that depend only on the distance between the NFRs located at the 5' and 3' gene ends. In the first type, this distance constrains in vivo the positioning of n nucleosomes regularly organized in a "crystal-like" array. In the second type, this distance is such that the corresponding genes can accommodate either n or (n + 1) nucleosomes, thereby displaying two possible crystal-like arrays of n weakly compacted or n + 1 highly compacted nucleosomes. This adaptability confers "bi-stable" properties to chromatin and is a key to its dynamics. Compared to crystal-like genes, bi-stable genes present higher transcriptional plasticity, higher sensitivity to chromatin regulators, higher H3 turnover rate, and lower H2A.Z enrichment. The results strongly suggest that transcription elongation is facilitated by higher chromatin compaction. The data allow us to propose a new paradigm of transcriptional control mediated by the stability and the level of compaction of the intragenic chromatin architecture and open new ways for investigating eukaryotic gene expression regulation