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International audience; La spondyloarthrite (SpA) est un rhumatisme inflammatoire chronique d’étiologie inconnue dont la survenue résulte de l’interaction de facteurs de prédisposition environnementaux et génétiques. Malgré des avancées récentes, une large fraction de la prédisposition génétique à la SpA demeure inexpliquée. Plusieurs mécanismes ont été proposés pour expliquer cette part d’héritabilité manquante, tels que l’épigénétique, qui peut jouer un rôle à l’interface entre facteurs génétiques et environnementaux de susceptibilité. L’épigénétique se réfère aux variations de l’expression génique qui n’impliquent aucun changement de la séquence d’ADN. Les mécanismes épigénétiques comprennent principalement la méthylation de l’ADN, les modifications des histones et les ARN non codants. La perturbation de l’un de ces systèmes peut conduire à une altération de l’expression génique susceptible de favoriser le développement de la maladie. Grâce aux récents progrès technologiques, on observe un intérêt croissant pour le domaine de l’épigénétique dans le contexte des maladies complexes comme la SpA. Cependant, les études épigénétiques sont confrontées à des obstacles méthodologiques qui limitent l’interprétation de leurs résultats : petite taille des échantillons, absence de confirmation des résultats, choix inapproprié des témoins, choix inadéquat du type cellulaire/tissulaire. Dans le futur, l’association de l’épigénétique aux autres données « -omiques » permettra de mieux comprendre la pathogénie de la SpA. Ces problématiques doivent être résolues avant d’envisager l’utilisation des marques épigénétiques en routine clinique, en tant que biomarqueurs ou cibles médicamenteuses.

Spondyloarthritis (SpA) is a chronic inflammatory disorder resulting from a combination of genetic predisposition and environmental factors. Despite recent advances, a substantial fraction of its genetic basis remains poorly understood. Several mechanisms have been proposed to account for this unexplained heritability, including epigenetics which can play a role at the interface between genetic and environmental susceptibility factors. Epigenetics refers to changes in gene expression that are not encoded in the DNA sequence itself. Such mechanisms may include DNA methylation, histone modifications and non-coding RNAs. Disruption of one of these systems can lead to inappropriate gene expression, which in turn might favour the development of disease. Thanks to recent technological progress, there has been a growing interest in the field of epigenetics in complex diseases, including SpA. However, epigenetic studies face some methodological limitations that hamper interpretation of their results: small sample size, absence of biological replication, lack of adequate controls for potential confounders, studies not performed in the most relevant cell/tissues. In the future, integration of epigenetics with other "omics" data will probably be necessary to improve our understanding of SpA pathogenesis. These issues need to be addressed before considering the use of epigenetic marks in clinical routine, as biomarkers or as drug targets.

The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS — a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.

Motivation Multi-scale modeling of biological systems requires integration of various information about genes and proteins that are connected together in networks. Spatial, temporal and functional information is available; however, it is still a challenge to retrieve and explore this knowledge in an integrated, quick and user-friendly manner. Results We present GEMMER (GEnome-wide tool for Multi-scale Modeling data Extraction and Representation), a web-based data-integration tool that facilitates high quality visualization of physical, regulatory and genetic interactions between proteins/genes in Saccharomyces cerevisiae. GEMMER creates network visualizations that integrate information on function, temporal expression, localization and abundance from various existing databases. GEMMER supports modeling efforts by effortlessly gathering this information and providing convenient export options for images and their underlying data. Availability and implementation GEMMER is freely available at http://gemmer.barberislab.com. Source code, written in Python, JavaScript library D3js, PHP and JSON, is freely available at https://github.com/barberislab/GEMMER. Supplementary information Supplementary data are available at Bioinformatics online.

The spatial organization of genomes is based on their hierarchical compartmentalization in topological domains. There is growing evidence that bacterial genomes are organized into insulated domains similar to the Topologically Associating Domains (TADs) detected in eukaryotic cells. Chromosome conformation capture (3C) technologies are used to analyze in vivo DNA proximity based on ligation of distal DNA segments crossed-linked by bridging proteins. By combining 3C and high-throughput sequencing, the Hi-C method reveals genome-wide interactions within topological domains and global genome structure as a whole. This chapter provides detailed guidelines for the preparation of Hi-C sequencing libraries for bacteria.

We present data on cell-to-cell variability (“‘noise”') of gene expression in human cells, obtained through a combination of single-molecule mRNA FISH and single-cell volume measurements. We find that noise in terms of mRNA numbers exceeds the noise in terms of mRNA concentration. This study provides an improved method to determine gene expression noise., Transcriptional stochasticity can be measured by counting the number of mRNA molecules per cell. Cell-to-cell variability is best captured in terms of concentration rather than molecule counts, because reaction rates depend on concentrations. We combined single-molecule mRNA counting with single-cell volume measurements to quantify the statistics of both transcript numbers and concentrations in human cells. We compared three cell clones that differ only in the genomic integration site of an identical constitutively expressed reporter gene. The transcript number per cell varied proportionally with cell volume in all three clones, indicating concentration homeostasis. We found that the cell-to-cell variability in the mRNA concentration is almost exclusively due to cell-to-cell variation in gene expression activity, whereas the cell-to-cell variation in mRNA number is larger, due to a significant contribution of cell volume variability. We concluded that the precise relationship between transcript number and cell volume sets the biological stochasticity of living cells. This study highlights the importance of the quantitative measurement of transcript concentrations in studies of cell-to-cell variability in biology.

Enzymology tends to focus on highly specific effects of substrates, allosteric modifiers, and products occurring at low concentrations, because these are most informative about the enzyme's catalytic mechanism. We hypothesized that at relatively high in vivo concentrations, important molecular monitors of the state of living cells, such as ATP, affect multiple enzymes of the former and that these interactions have gone unnoticed in enzymology.We test this hypothesis in terms of the effect that ATP, ADP, and AMP might have on the major free-energy delivering pathway of the yeast Saccharomyces cerevisiae. Assaying cell-free extracts, we collected a comprehensive set of quantitative kinetic data concerning the enzymes of the glycolytic and the ethanol fermentation pathways. We determined systematically the extent to which the enzyme activities depend on the concentrations of the adenine nucleotides. We found that the effects of the adenine nucleotides on enzymes catalysing reactions in which they are not directly involved as substrate or product, are substantial. This includes effects on the Michaelis-Menten constants, adding new perspective on these, 100 years after their introduction. (C) 2013 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

The effective volume occupied by the genomes of all forms of life far exceeds that of the cells in which they are contained. Therefore, all organisms have developed mechanisms for compactly folding and functionally organizing their genetic material. Through recent advances in fluorescent microscopy and 3C-based technologies, we finally have a first glimpse into the complex mechanisms governing the 3-D folding of genomes. A key feature of genome organization in all domains of life is the formation of DNA loops. Here, we describe the main players in DNA organization with a focus on DNA-bridging proteins. Specifically, we discuss the properties of the bacterial DNA-bridging protein H-NS. Via two different modes of binding to DNA, this protein is a key driver of bacterial genome organization and provides a link between 3-D organization and transcription regulation. Importantly, H-NS function is modulated in response to environmental cues, which are translated into adapted gene expression patterns. We delve into the mechanisms underlying DNA looping and explore the complex and subtle modulation of these diverse, yet difficult-to-study, structures. DNA looping is universal and a conserved mechanism of genome organization throughout all domains of life.

Systems Biology brings the potential to discover fundamental principles of Life that cannot be discovered by considering individual molecules. This chapter discusses a number of early, more recent, and upcoming discoveries of such network principles. These range from the balancing of fluxes through metabolic networks, the potential of those networks for truly individualized medicine, the time dependent control of fluxes and concentrations in metabolism and signal transduction, the ways in which organisms appear to regulate metabolic processes vis-A -vis limitations therein, tradeoffs in robustness and fragility, and a relation between robustness and time dependences in the cell cycle. The robustness considerations will lead to the issue whether and how evolution has been able to put in place design principles of control engineering such as infinite robustness and perfect adaptation in the hierarchical biochemical networks of cell biology © 2014 Elsevier Inc. All rights reserved.

We describe the identification and detailed expression pattern of a second Drosophila Sox gene, SoxNeuro (SoxN), highly related to mammalian group B Sox1, 2, 3 genes. SoxN is expressed in a highly dynamic pattern during embyogenesis, being associated with the development of the central nervous system (CNS), from the early steps onwards. We present strong evidence that the early SoxN neuroectoderm expression is controlled by the zygotic dorso-ventral patterning genes (dpp, sog, brk, twi).

Although the distribution of DNA-binding proteins inside the cell nucleus can be analyzed by immunolabeling or by tagging proteins with GFP, we cannot establish whether the protein is bound to DNA or not. Here, we describe a novel approach that allows imaging of the in situ interaction between a GFP-fusion protein and DNA in the cell nucleus, using fluorescence resonance energy transfer (FRET). We used fluorescence lifetime imaging microscopy (FLIM) as a reliable tool to detect protein in contact with DNA. The method was successfully applied to the DNA-binding proteins histone H2B and the glucocorticoid receptor and to the heterochromatin-associated proteins HP1alpha and HP1beta.Copyright © 2005 Elsevier Inc.

We have identified a novel Sox gene in zebrafish (Danio rerio), Sox31, closely related to mammalian group B Sox genes. The gene is maternally expressed. Zygotic transcription starts at gastrulation, in the presumptive neuroectoderm. Later, expression is restricted to the developing central nervous system, including forebrain, midbrain, hindbrain and spinal cord.

SOX proteins contain a conserved HMG-related DNA-binding domain. They fulfil essential functions during the development of animals. Mutations in several SOX genes have been implicated in human diseases. We present here a new set of PCR primers designed to amplify a broad range of SOX HMG-box sequences. These primers facilitated the cloning of several new SOX HMG boxes from human genomic DNA, revealing unexpected complexity of the SOX gene family.