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The folding of nucleosome chains influences DNA availability for functional interactions necessary to the regulation of transcription, DNA replication and repair. Despite models based on in vitro studies, the nucleosome chain geometry within the crowded cell nucleus remains elusive. Using cryo-electron tomography and deep learning-based denoising, we directly observed the path of nucleosomal and linker DNA in situ in unstained flash-frozen Drosophila embryos. We quantified linker length and curvature characterizing a disordered zig-zag chromatin folding motif, with a low degree of linker bending. Additionally, nucleosome conformational variability with non-canonical structures and sub-nucleosomal particles were seen as individual objects, without structure averaging, highlighting the high structural heterogeneity of native chromatin.One-Sentence SummaryCryo-ET reveals local zig-zag motifs in interphase chromatin, a range of nucleosome conformations, and sub-nucleosomal particles.

Face à la tyrannie éditoriale du roman dans le champ de la fiction américaine, un certain nombre d’auteurs de la première moitié du XXe siècle s’écartent des conventions formelles qui président aux modalités du récit en explorant les possibilités offertes par le « cycle de nouvelles » : dans le cadre de ce format narratif singulier, chaque nouvelle du cycle peut se lire de manière autonome, mais son sens se trouve modifié et/ou accru par les rapports qu’elle entretient avec les autres textes du volume. La lecture se fait sur un mode discontinu et fragmentaire, où seuls divers types d’échos peuvent inciter à reconstruire une unité qui n’est pas donnée au départ, et qui sollicite – beaucoup plus fortement que le roman – la participation active du lecteur. Cet article se propose d’analyser la complexité des jeux de format induits par la lecture d’un cycle de nouvelles exemplaire à plusieurs titres : The Golden Apples de Eudora Welty (1949). Comment ce format cyclique instable interagit-il avec la ligne thématique du livre, tendue entre liaison et déliaison et, du même coup, en quoi peut-il mener à une réflexion plus large sur les modalités de réception de cet objet narratif en rupture avec les normes romanesques ? In reaction to the novel’s editorial tyranny in American fiction, a number of writers in the first half of the 20th century shifting away from conventional narrative forms explored the possibilities of the short story cycle : within this peculiar narrative format, each story can be read independently but its meaning is modified and/or expanded through its relations to the other texts composing the volume. Reading becomes discontinuous and fragmentary. Various types of echoes invite the reader to reconstruct some degree of unity as such unity is not provided from the start, which requires a much higher level of reader participation than in the case of a novel. This article proposes to analyze the complex ways in which Eudora Welty plays with such a format in her own 1949 short story cycle The Golden Apples. How does this unstable cyclical format interact with the book’s thematics, oscillating between interrelatedness and separateness and, as a result, how does it challenge the reader’s own reception of this narrative construct that turns its back on novelistic norms?

International audience; Is it possible to measure the dispersion of ex ante chances (i.e., chances “before the event”) among people, be it gambling, health, or social opportunities? We explore this question and provide some tools, including a statistical test, to evidence the actual dispersion of ex ante chances in various areas, with a focus on chronic diseases. Using the principle of maximum entropy, we derive the distribution of the risk of becoming ill in the global population as well as in the population of affected people. We find that affected people are either at very low risk, like the overwhelming majority of the population, but still were unlucky to become ill, or are at extremely high risk and were bound to become ill.

La molécule d'ADN est le support physique de l'information génétique. Ce long polymère est compacté grâce à des protéines pour former les chromosomes. Ce repliement assure la régulation de l’expression des gènes au cours de la vie des cellules. La biochimie des chromosomes est un sujet d'intenses investigations, mais il apparait aujourd'hui que les propriétés physiques des chromosomes sont aussi au coeur de leur fonctionnement. Ces propriétés peuvent être décrites en combinant physique statistique et physique des polymères en solution. Dans cet article, nous présentons les méthodes multi-échelles que nous avons développées pour reconstruire et animer l'architecture fonctionnelle des chromosomes.

DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion and structural properties inferred from yeast chromosomes determined with chromosome conformation capture techniques (specifically, Hi-C). We hence introduce the Rouse model with Transient Internal Contacts (RouseTIC), in which random association and dissociation occurs along the chromosome contour. The parametrization of this model by fitting motion and Hi-C data allows us to measure the kinetic parameters of the contact formation reaction. Chromosome contacts appear to be transient; associated to a lifetime of seconds and characterized by an attractive energy of –0.3 to –0.5 kBT. We suggest attributing this energy to the occurrence of histone tail-DNA contacts and notice that its amplitude sets chromosomes in ‘theta’ conditions, in which they are poised for compartmentalization and phase separation.

International audience; The dynamics of single DNA molecules conveyed in a viscoelastic fluid flow with an opposing electrophoretic force are investigated by fluorescence microscopy. For balanced hydrodynamic and electrophoretic forces, DNA is confined near the walls with a much smaller elongation than in bulk shear flows. Furthermore, we observe that DNA extension is characterized by intermittent fluctuations, the characteristic time scale of which depends on the flow velocity. A model based on Rouse dynamics explains the contraction of the molecule by the coupling of monomer motion in the transverse and longitudinal directions to the flow induced by transverse viscoelastic forces. Using simulations, we suggest that the occurrence of intermittent fluctuations is analogous to tumbling dynamics characterized by the cyclic spooling motion of end monomers about the molecule center of mass

Additional file 1: Figure S1. Mean and median radii of gyration from the dataset of Boettiger et al. [2] with corresponding boxplots. Figure S2. Selected histograms from the on-lattice simulations with the corresponding theoretical distributions. Figures S3, S4, S5. Parameter distributions inferred from data by Bayesian analysis for active, inactive and repressed domains, respectively. Figures S6, S7, S8. Data histograms with the corresponding theoretical distributions obtained using the fitted parameters for active, inactive and repressed domains, respectively. Figure S9. Gyration radius experimental medians and boxplots with the corresponding fitting theoretical curves.

BackgroundLocalized functional domains within chromosomes, known astopologically associating domains(TADs), have been recently highlighted. InDrosophila, TADs are biochemically defined by epigenetic marks, this suggesting that the 3D arrangement may be the “missing link” between epigenetics and gene activity. Recent observations (Boettiger et al., Nature 2016) provide access to structural features of these domains with unprecedented resolution thanks to super-resolution experiments. In particular, they give access to thedistributionof the radii of gyration for domains of different linear length and associated with different transcriptional activity states: active, inactive or repressed. Intriguingly, the observed scaling laws lack consistent interpretation in polymer physics.ResultsWe develop a new methodology conceived to extract the best information from such super-resolution data by exploiting the whole distribution of gyration radii, and to place these experimental results on a theoretical framework. We show that the experimental data are compatible with thefinite-sizebehavior of aself-attracting polymer. The same generic polymer model leads to quantitative differences between active, inactive and repressed domains. Active domains behave as pure polymer coils, while inactive and repressed domains both lie at the coil-globule crossover. For the first time, the “colo-specificity” of both the persistence length and the mean interaction energy are estimated, leading to important differences between epigenetic states.ConclusionsThese results point toward a crucial role of criticality to enhance the system responsivity, resulting in both energy transitions and structural rearrangements. We get strong indications that epigenetically induced changes in nucleosome-nucleosome interaction can cause chromatin to shift between different activity states.

RNA polymerase (RNAP) is, in its elongation phase, an emblematic example of a molecular motor whose activity is highly sensitive to DNA supercoiling. After a review of DNA supercoiling basic features, we discuss how supercoiling controls polymerase velocity, while being itself modified by polymerase activity. This coupling is supported by single-molecule measurements. Physical modeling allows us to describe quantitatively how supercoiling and torsional constraints mediate a mechanical coupling between adjacent polymerases. On this basis, we obtain a description that may explain the existence and functioning of RNAP convoys.

RNA polymerase (RNAP) is, in its elongation phase, an emblematic example of a molecular motor whose activity is highly sensitive to DNA supercoiling. After a review of DNA supercoiling basic features, we discuss how supercoiling controls polymerase velocity, while being itself modified by polymerase activity. This coupling is supported by single-molecule measurements. Physical modeling allows us to describe quantitatively how supercoiling and torsional constraints mediate a mechanical coupling between adjacent polymerases. On this basis, we obtain a description that may explain the existence and functioning of RNAP convoys.

Chromosome mechanical properties determine DNA folding and dynamics, and underlie all major nuclear functions. Here we combine modeling and real-time motion tracking experiments to infer the physical parameters describing chromatin fibers. In vitro, motion of nucleosome arrays can be accurately modeled by assuming a Kuhn length of 35-55 nm. In vivo, the amplitude of chromosome fluctuations is drastically reduced, and depends on transcription. Transcription activation increases chromatin dynamics only if it involves gene relocalization, while global transcriptional inhibition augments the fluctuations, yet without relocalization. Chromatin fiber motion is accounted for by a model of equilibrium fluctuations of a polymer chain, in which random contacts along the chromosome contour induce an excess of internal friction. Simulations that reproduce chromosome conformation capture and imaging data corroborate this hypothesis. This model unravels the transient nature of chromosome contacts, characterized by a life time of ∼2 seconds and a free energy of formation of ∼1 kBT.

D’un bout à l’autre de sa courte carrière, le photographe américain Ralph Eugene Meatyard (1925-1972) incorpore à ses images diverses manifestations physiques du signe écrit, voire des traces mimant le geste de l’écriture. Qu’il s’agisse d’affiches, de graffiti, de pancartes, de journaux, de lettrage peint au bord de l’effacement, ces fantômes de textes accompagnent des présences humaines (famille, amis) avec lesquelles ils semblent entretenir un rapport mystérieux. D’autres photographies plus abstraites captant le tracé calligraphique de la lumière sur l’eau, ou présentant des formes naturelles minimales (brindilles, traces de gel) évoquent les signes d’une écriture indéchiffrable. Cet article se propose d’analyser la complexité des modalités de réception que mettent en jeu ces stratégies intersémiotiques chez un photographe profondément influencé par une fine connaissance de la littérature et par la fréquentation d’écrivains vivant, comme lui, dans le Sud des Etats-Unis dans les années 1950 et 1960. Throughout his short career, American photographer Ralph Eugene Meatyard (1925-1972) incorporated into his pictures various physical manifestations of written signs, as well as traces mimicking the act of writing. Posters, graffiti, street signs, newspapers, fading painted letters appear as ghostly texts in company with human beings (family, friends) with which they seem to engage in a mysterious relationship. Even his more abstract pictures recording calligraphic shapes drawn by light on water, or showing minimalistic natural forms (twigs, marks of frost) are reminiscent of some undecipherable handwriting. This paper proposes to analyze the complex modes of reception generated by such intersemiotic strategies on the part of a photographer who was strongly influenced by his vast knowledge of literature and many literary friendships formed in the context of the American South in the 1950s and 1960s.

Live-cell imaging has revealed unexpected features of gene expression. Here using improved single-molecule RNA microscopy, we show that synthesis of HIV-1 RNA is achieved by groups of closely spaced polymerases, termed convoys, as opposed to single isolated enzymes. Convoys arise by a Mediator-dependent reinitiation mechanism, which generates a transient but rapid succession of polymerases initiating and escaping the promoter. During elongation, polymerases are spaced by few hundred nucleotides, and physical modelling suggests that DNA torsional stress may maintain polymerase spacing. We additionally observe that the HIV-1 promoter displays stochastic fluctuations on two time scales, which we refer to as multi-scale bursting. Each time scale is regulated independently: Mediator controls minute-scale fluctuation (convoys), while TBP-TATA-box interaction controls sub-hour fluctuations (long permissive/non-permissive periods). A cellular promoter also produces polymerase convoys and displays multi-scale bursting. We propose that slow, TBP-dependent fluctuations are important for phenotypic variability of single cells., HIV-1 viral gene expression stochastically switches between active and inactive states. Here, using improved single molecule RNA microscopy, the authors show that HIV-1 RNA stochastic transcription is achieved by groups of closely spaced polymerases, and is regulated by Mediator and TBP at different time scales.

In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the daughter cells. This intriguing phenomenon is achieved by a variety of processes that have been collectively termed epigenetics: the stable and inheritable changes in gene expression patterns. This article reviews the extremely rich and exquisitely multi-scale physical mechanisms that govern the biological processes behind the initiation, spreading and inheritance of epigenetic states. These include not only the changes in the molecular properties associated with the chemical modifications of DNA and histone proteins, such as methylation and acetylation, but also less conventional ones, such as the physics that governs the three-dimensional organization of the genome in cell nuclei. Strikingly, to achieve stability and heritability of epigenetic states, cells take advantage of many different physical principles, such as the universal behavior of polymers and copolymers, the general features of non-equilibrium dynamical systems, and the electrostatic and mechanical properties related to chemical modifications of DNA and histones. By putting the complex biological literature under this new light, the emerging picture is that a limited set of general physical rules play a key role in initiating, shaping and transmitting this crucial "epigenetic landscape". This new perspective not only allows to rationalize the normal cellular functions, but also helps to understand the emergence of pathological states, in which the epigenetic landscape becomes dysfunctional., 34 pages, 13 figures

Using a simple geometric model, we propose a general method for computing the linking number of the DNA embedded in chromatin fibers. The relevance of the method is reviewed through the single molecule experiments that have been performed in vitro with magnetic tweezers. We compute the linking number of the DNA in the manifold conformational states of the nucleosome which have been evidenced in these experiments and discuss the functional dynamics of chromosomes in the light of these manifold states.

The ability of cells to pack, use and duplicate DNA remains one of the most fascinating questions in biology. To understand DNA organization and dynamics, it is important to consider the physical and topological constraints acting on it. In the eukaryotic cell nucleus, DNA is organized by proteins acting as spools on which DNA can be wrapped. These proteins can subsequently interact and form a structure called the chromatin fibre. Using a simple geometric model, we propose a general method for computing topological properties ( twist , writhe and linking number ) of the DNA embedded in those fibres. The relevance of the method is reviewed through the analysis of magnetic tweezers single molecule experiments that revealed unexpected properties of the chromatin fibre. Possible biological implications of these results are discussed.

International audience; Genomic DNA in eukaryotic cells is organized in supercoiled chromatin fibers, which undergo dynamic changes during such DNA metabolic processes as transcription or replication. Indeed, DNA-translocating enzymes like polymerases produce physical constraints in vivo. We used single-molecule micromanipulation by magnetic tweezers to study the response of chromatin to mechanical constraints in the same range as those encountered in vivo. We had previously shown that under positive torsional constraints, nucleosomes can undergo a reversible chiral transition toward a state of positive topology. We demonstrate here that chromatin fibers comprising linker histones present a torsional plasticity similar to that of naked nucleosome arrays. Chromatosomes can undergo a reversible chiral transition toward a state of positive torsion (reverse chromatosome) without loss of linker histones.

(Received February 24, 2011)DNA transaction events occurring during a cell cycle (transcription, repair, replication)are always associated with severe topological constraints on the double helix. However, sincenuclear DNA is bound to various proteins (including histones) that control its accessibilityand 3D organization, these topological constraints propagate or accumulate on a chromatinsubstrate. This paper focuses on chromatin fiber response to physiological mechanical con-straints expected to occur during transcription elongation. We will show in particular howrecent single molecule techniques help us to understand how chromatin conformational dy-namics could manage harsh DNA supercoiling changes.

Genetic and epigenetic information in eukaryotic cells is carried on chromosomes, basically consisting of large compact supercoiled chromatin fibers. Micromanipulations have recently led to great advances in the knowledge of the complex mechanisms underlying the regulation of DNA transaction events by nucleosome and chromatin structural changes. Indeed, magnetic and optical tweezers have allowed opportunities to handle single nucleosomal particles or nucleosomal arrays and measure their response to forces and torques, mimicking the molecular constraints imposed in vivo by various molecular motors acting on the DNA. These challenging technical approaches provide us with deeper understanding of the way chromatin dynamically packages our genome and participates in the regulation of cellular metabolism.

During eukaryotic transcription, RNA-polymerase activity generates torsional stress in DNA, having a negative impact on the elongation process. Using our previous studies of chromatin fiber structure and conformational transitions, we suggest that this torsional stress can be alleviated, thanks to a tradeoff between the fiber twist and nucleosome conformational transitions into an activated state named “reversome”. Our model enlightens the origin of polymerase pauses, and leads to the counterintuitive conclusion that chromatin-organized compaction might facilitate polymerase progression. Indeed, in a compact and well-structured chromatin loop, steric hindrance between nucleosomes enforces sequential transitions, thus ensuring that the polymerase always meets a permissive nucleosomal state.

This study analyzes various strategies of suspension in one of Eudora Welty’s early stories, “A Curtain of Green”. Most of them pave the way for aesthetic choices to be confirmed in her later works : narrative discontinuity, visual screens, diegetic indetermination and an ambivalent use of intertextuality.

Chromatin structure is a powerful tool to regulate eukaryotic transcription. Moreover, nucleosomes are constantly remodeled, disassembled, and reassembled in the body of transcribed genes. Here we propose a general model that explains, in quantitative terms, how transcription elongation affects nucleosome structure at a distance as a result of the positive torque the polymerases create as they translocate along DNA templates.

Ever since the discovery of the nucleosome in 1974, scientists have stumbled upon discrete particles in which DNA is wrapped around histone complexes of different stoichiometries: octasomes, hexasomes, tetrasomes, “split” half-nucleosomes, and, recently, bona fide hemisomes. Do all these particles exist in vivo? Under what conditions? What is their physiological significance in the complex DNA transactions in the eukaryotic nucleus? What are their dynamics? This review summarizes research spanning more than three decades and provides a new meaning to the term “nucleosome.” The nucleosome can no longer be viewed as a single static entity: rather, it is a family of particles differing in their structural and dynamic properties, leading to different functionalities.

International audience; Cell survival is conventionally defined as the capability of irradiated cells to produce colonies. It is quantified by the clonogenic assays that consist in determining the number of colonies resulting from a known number of irradiated cells. Several mathematical models were proposed to describe the survival curves, notably from the target theory. The Linear-Quadratic (LQ) model, which is to date the most frequently used model in radiobiology and radiotherapy, dominates all the other models by its robust- ness and simplicity. Its usefulness is particularly important because the ratio of the values of the adjustable parameters, α and β, on which it is based, predicts the occurrence of post-irradiation tissue reactions. However, the biological interpretation of these parameters is still unknown.Throughout this review, we revisit and discuss historically, mathematically and biologically, the different models of the radiation action by providing clues for resolving the enigma of the LQ model.

International audience; BACKGROUND: Numerous genetic and environmental risk factors play a role in human complex genetic disorders (CGD). However, their complex interplay remains to be modelled and explained in terms of disease mechanisms.METHODS AND FINDINGS: Crohn's Disease (CD) was modeled as a modular network of patho-physiological functions, each summarizing multiple gene-gene and gene-environment interactions. The disease resulted from one or few specific combinations of module functional states. Network aging dynamics was able to reproduce age-specific CD incidence curves as well as their variations over the past century in Western countries. Within the model, we translated the odds ratios (OR) associated to at-risk alleles in terms of disease propensities of the functional modules. Finally, the model was successfully applied to other CGD including ulcerative colitis, ankylosing spondylitis, multiple sclerosis and schizophrenia.CONCLUSION: Modeling disease incidence may help to understand disease causative chains, to delineate the potential of personalized medicine, and to monitor epidemiological changes in CGD.

DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical condensation forces have been used to estimate the amplitude of the attractive DNA-DNA interactions. Here, to describe these experiments, we developed an analytical model and a rigid body Langevin dynamics assay to investigate the behavior of a polymer with self-interactions, in the presence of a traction force applied at its extremities. We model self-interactions using a pairwise attractive potential, thereby treating the counterions implicitly. The analytical model allows to accurately predict the equilibrium structures of toroidal and rod-like condensed structures, and the dependence of the critical condensation force on the DNA length. We find that the critical condensation force depends strongly on the length of the DNA, and finite-size effects are important for molecules of length up to 10^5 {\mu}m. Our Langevin dynamics simulations show that the force-extension behavior of the rod-like structures is very different from the toroidal ones, so that their presence in experiments should be easily detectable. In double-stranded DNA condensation experiments, the signature of the presence of rod-like structures was not unambiguously detected, suggesting that the polyamines used to condense DNA may protect it from bending sharply as needed in the rod-like structures, Comment: 10 pages, 7 figures

The biological functions played by the nucleus of eukaryotic cells and especially those involved in cellular differentiation not only depend on the genomic sequence but also on all the proteins which form the nucleo-protein complex named chromatin. The tridimensional organization of this huge polymer involves many structural levels, the most basic one being the nucleosome. Nucleosomes further organize into the so-called 30 nm fiber, which, according to recent works, is likely to be the main functional level of chromatin. We wish here to propose a plausible structure for the 30 nm chromatin fiber that could explain its functional role. In our model, silenced chromatin is locked by nucleosome stacking interactions. This is achieved by a conformational transition within the nucleosome core particle (NCP) which allows nucleosomes to stack along two helices without bending the DNA linkers. We used molecular modeling to check that this conformational transition was plausible. Then we proposed to modify the well-known two-angle model according to these atomic level results. The emerging picture is an allosteric behavior of the nucleosomes induced by their collective organization within the 30 nm chromatin fiber.

Crohn's disease (CD) is a complex genetic disorder for which aetiology is unknown. Recently, genetic factors for susceptibility have been described. Several genetic loci have been mapped and partially explain the familial aggregations of the disease. However, environmental factors may also contribute to these aggregations. We considered that if the role of non-genetic factors was negligible, CD patients would be randomly distributed in sibships with multiple affected siblings. On the other hand if there was a significant environmental contribution, the siblings would be affected non-randomly over exposure status. In order to test this hypothesis, we studied 102 sibships with two or more affected siblings. A statistical test, named Cluster of Affected Sibling Test or CAST, was developed, based on the exact calculation of the probability of observing a given number of clusters of affected siblings in multiplex families. The null hypothesis of a random distribution of affected siblings was rejected (P=0.005). The observed excess of affected sibling clusters indicates that birth order influences the disease status. Considering that an adjacent order of birth is a global estimate of environmental sharing, this observation strongly suggests that environmental factors contribute to the observed familial aggregations of the disease. This observation provides evidence that familial CD is a relevant tool for further studies of environmental factors and gene-environment interaction. More generally, the CAST statistics may be widely applicable to estimate the involvement of environmental factors in the aetiology of other binary traits which may be observed in multiple members of the same sibship.

Background In higher eukaryotes, the genome is partitioned into large "Topologically Associating Domains" (TADs) in which the chromatin displays favoured long-range contacts. While a crumpled/fractal globule organization has received experimental supports at higher-order levels, the organization principles that govern chromatin dynamics within these TADs remain unclear. Using simple polymer models, we previously showed that, in mouse liver cells, gene-rich domains tend to adopt a statistical helix shape when no significant locus-specific interaction takes place. Results Here, we use data from diverse 3C-derived methods to explore chromatin dynamics within mouse and Drosophila TADs. In mouse Embryonic Stem Cells (mESC), that possess large TADs (median size of 840 kb), we show that the statistical helix model, but not globule models, is relevant not only in gene-rich TADs, but also in gene-poor and gene-desert TADs. Interestingly, this statistical helix organization is considerably relaxed in mESC compared to liver cells, indicating that the impact of the constraints responsible for this organization is weaker in pluripotent cells. Finally, depletion of histone H1 in mESC alters local chromatin flexibility but not the statistical helix organization. In Drosophila, which possesses TADs of smaller sizes (median size of 70 kb), we show that, while chromatin compaction and flexibility are finely tuned according to the epigenetic landscape, chromatin dynamics within TADs is generally compatible with an unconstrained polymer configuration. Conclusions Models issued from polymer physics can accurately describe the organization principles governing chromatin dynamics in both mouse and Drosophila TADs. However, constraints applied on this dynamics within mammalian TADs have a peculiar impact resulting in a statistical helix organization. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1786-8) contains supplementary material, which is available to authorized users.