L’environnement intracellulaire est densément peuplé et extrêmement organisé. Plusieurs processus de transport y ont lieu : la marche des moteurs moléculaires sur les microtubules et les microfilaments d’actine, ainsi que la translocation d’autres moteurs moléculaires comme l’ARN polymérase sur l’ADN et les ribosomes sur l’ARN messager (ARNm). Dans cette thèse, nous étudions la translocation du ribosome sur l’ARNm permettant la traduction du code génétique en protéines et qui, d’un point de vue physique, est un processus de transport dirigé à une dimension. Il s’agit d’un phénomène non-linéaire, stochastique et hors-équilibre thermodynamique qui relève de la physique statistique hors-équilibre. La traduction génétique est une étape de l’expression des gènes régulée par plusieurs mécanismes qui sont encore mal connus. En apportant une étude physique de la cinétique de traduction, nous espérons contribuer à une meilleure compréhension de la régulation de la production des protéines pendant cette étape. Une telle compréhension devrait impacter également la recherche médicale en ce qui concerne les maladies liées à une dérégulation de l’expression génétique comme le cancer et les maladies neurodégénératives.Un premier chapitre est consacré au contexte biologique de la traduction ainsi qu’à la brève description de l’expérience de ribosome profiling, une méthode de séquençage haut débit effectuée par nos collègues biologistes. Elle permet, depuis une dizaine d’années, une avancée considérable de la recherche sur la traduction, mais la complexité du système mesuré nécessite un travail de modélisation physico-mathématique plus poussé.Le deuxième chapitre décrit le modèle paradigmatique des transports dirigés à une dimension, le modèle de gaz sur réseau Totally Asymmetric Simple Exclusion Process (TASEP) et ses variantes, plus proches de la translocation ribosomale, sont étudiés. Nous montrons qu’une particule étendue engendre des effets d’exclusions non négligeables en phase basse densité. En particulier, l’exclusion au départ de la traduction a l’effet le plus important sur la densité moyenne le long du réseau lorsque le rapport du taux d’initiation sur le taux de saut de la particule est inférieur ou égal à 0,1, tandis que lorsque ce rapport est plus élevé, un effet de bord en sortie du réseau devient aussi non négligeable.Dans le troisième chapitre, nous modélisons l’ensemble d’ARNm, séquencé dans l’expérience de ribosome profiling (ou Ribo-Seq), par un modèle balistique où les ribosomes sont des particules ponctuelles se déplaçant de manière déterministe sur des filaments ayant, ce qui est rarement considéré, une durée de vie finie. Nous montrons que, pour des paramètres ayant des valeurs biologiques typiques, l’effet de temps de vie fini sur la densité de ribosomes est négligeable lorsque l’on considère l’ensemble des ARNm, les polysomes, mais qu’il devient important lorsque l’on considère des populations d’ARNm séparées par leur nombre de ribosomes, les k-somes. Nous caractérisons précisément cet effet par une analyse paramétrique, ce qui nous permet de définirtrois régimes de dégradation de l’ARNm.Dans le dernier chapitre, nous mettons en évidence pour la première fois à notre connaissance cet effet de temps de vie fini sur des profils Ribo-Seq de monosomes, disomes , trisomes et tétrasomes (k-somes pour k=1,2,3 et 4). Nous comparons ensuite notre modèle avec plusieurs milliers de profils Ribo-Seq effectués par nos collaborateurs biologistes de l’IGF et bioinformaticiens du LIRMM pour observer que notre modèle donne une bonne description des profils k-somes. Enfin, nous proposons dans ce chapitre une méthode de déduction des paramètres cinétiques de la traduction, le taux d’initiation et le taux de saut du ribosome à l’aide de la densité monosome et de la densité polysome.

Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribo-sequencing (Ribo-seq) technique. In this case an inverse fit gives access to the kinetic rates: the position-dependent speeds and the entry rate of ribosomes onto mRNA. The degradation rate is not, however, accounted for and experimental data from different experiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We solve analytically the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criteria for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) ribo-seq profiles enable us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.

Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribosome sequencing (Ribo-Seq) technique. In this case an inverse fit gives access to the kinetic rates: the position-dependent speeds and the entry rate of ribosomes into mRNA. The degradation rate is not, however, accounted for and experimental data from differentexperiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We analytically solve the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criterion for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) Ribo-Seq profiles enables us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.

Polycomb (Pc) group proteins are transcriptional regulators with key roles in development, cell identity and differentiation. Pc-bound chromatin regions form repressive domains that interact in 3D to assemble repressive nuclear compartments. Here, we used multiplexed chromatin imaging to investigate whether Pc compartments involve the clustering of multiple Pc domains during Drosophila development. Notably, 3D proximity between Pc targets is rare and involves predominantly pairwise interactions. These 3D proximities are particularly enhanced in segments where Pc genes are co-repressed. In addition, segment-specific expression of Hox Pc targets leads to their spatial segregation from Pc repressed genes. Finally, non-Hox Pc targets are proximal in regions where they are co-expressed. These results indicate that long-range Pc interactions are temporally and spatially regulated during differentiation and development but do not involve clustering of multiple distant Pc genes.

Although the polygonal shape of epithelial cells has been drawing the attention of scientists for several centuries, only a decade and a half ago it was demonstrated that distributions of polygon types (DOPTs) are similar in proliferative epithelia of many different plant and animal species. In this study, we show that hyper-proliferation of cancer cells disrupts this universal paradigm and results in randomly organized epithelial structures. Examining non-synchronized and synchronized HeLa cervix cells, we suppose that the spread of cell sizes is the main parameter controlling the DOPT in the cancer cell monolayers. To test this hypothesis, we develop a theory of morphologically similar random polygonal packings. By analysing differences between tumoural and normal epithelial cell monolayers, we conclude that the latter have more ordered structures because of their lower proliferation rates and, consequently, more effective relaxation of mechanical stress associated with cell division and growth. To explain the structural features of normal proliferative epithelium, we take into account the spread of cell sizes in the monolayer. The proposed theory also rationalizes some highly ordered unconventional post-mitotic epithelia.

Controlled motion and positioning of colloids and macromolecular complexes in a fluid, as well as catalytic particles in active environments, are fundamental processes in physics, chemistry and biology. Here we focus on an active biological system for which precise experimental results are available. Our work is fully inspired by studies of one of the most widespread and ancient mechanisms of liquid phase macromolecular segregation and positioning known in nature: bacterial DNA segregation systems. Efficient bacterial chromosome segregation typically requires the coordinated action of a three-component, fueled by adenosine triphosphate machinery called the partition complex. We can distinguish two steps: (i) a process of phase transition [2,3] to built a membraneless region of high protein concentration (partition complex) (ii) the action of molecular motor action upon the complex to create a chemical force.We present a phenomenological model [1] accounting for the dynamics of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simple linear reaction-diffusion equations with a volumetric chemophoresis force field that arises from protein-protein interactions and provides a physically viable mechanism for complex translocation. This description captures experimental observations: dynamic oscillations of complex components, complex separation and symmetrical positioning. The predictions of our model are in agreement with and provide substantial insight into recent experiments. From a non-linear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and travelling wave regimes triggered by the dynamical spontaneous breaking of rotational symmetry. We also discuss the phase transition mechanism giving rise to macromolecular assembly of proteins. Our predictions are compared to Super Resolution microscopy and microbiology experiments [1,2,3].[1] Walter J.-C., Dorignac J., Lorman V., Rech J., Bouet J.-Y., Nollmann M., Palmeri J., Parmeggiani A. and Geniet F., Phys. Rev. Lett. 119, 028101 (2017).[2] Debaugny R., Sanchez A., Rech J., Labourdette D., Dorignac J., Geniet F., Palmeri J., Parmeggiani A., Boudsocq, Leberre V., Walter* J.-C. and Bouet* J.-Y Mol. Syst. Biol. 14, e8516 (2018).[3] David G., Walter J.-C., Broedersz C., Dorignac J., Geniet F., Parmeggiani A., Walliser N.-O. and Palmeri J., Phys. Rev. Res. 2, 033377 (2020).