Annuaire de la recherche géographique francophone

Annuaire de la recherche géographique francophone

Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites

The positions of nucleosomes in eukaryotic genomes determine which parts of the DNA sequence are readily accessible for regulatory proteins and which are not. Genome-wide maps of nucleosome positions have revealed a salient pattern around transcription start sites, involving a nucleosome-free region (NFR) flanked by a pronounced periodic pattern in the average nucleosome density. While the periodic pattern clearly reflects well-positioned nucleosomes, the positioning mechanism is less clear. A recent experimental study by Mavrich et al. argued that the pattern observed in S. cerevisiae is qualitatively consistent with a `barrier nucleosome model', in which the oscillatory pattern is created by the statistical positioning mechanism of Kornberg and Stryer. On the other hand, there is clear evidence for intrinsic sequence preferences of nucleosomes, and it is unclear to what extent these sequence preferences affect the observed pattern. To test the barrier nucleosome model, we quantitatively analyze yeast nucleosome positioning data both up- and downstream from NFRs. Our analysis is based on the Tonks model of statistical physics which quantifies the interplay between the excluded-volume interaction of nucleosomes and their positional entropy. We find that although the typical patterns on the two sides of the NFR are different, they are both quantitatively described by the same physical model, with the same parameters, but different boundary conditions. The inferred boundary conditions suggest that the first nucleosome downstream from the NFR (the +1 nucleosome) is typically directly positioned while the first nucleosome upstream is statistically positioned via a nucleosome-repelling DNA region. These boundary conditions, which can be locally encoded into the genome sequence, significantly shape the statistical distribution of nucleosomes over a range of up to ~1000 bp to each side.Comment: includes supporting materia

CC9 Livestock-Associated Staphylococcus aureus Emerges in Bloodstream Infections in French Patients Unconnected With Animal Farming

We report 4 bloodstream infections associated with CC9 agr type II Staphylococcus aureus in individuals without animal exposure. We demonstrate, by microarray analysis, the presence of egc cluster, fnbA, cap operon, lukS, set2, set12, splE, splD, sak, epiD, and can, genomic features associated with a high virulence potential in human

Mechanics of the IL2RA Gene Activation Revealed by Modeling and Atomic Force Microscopy

Transcription implies recruitment of RNA polymerase II and transcription factors (TFs) by DNA melting near transcription start site (TSS). Combining atomic force microscopy and computer modeling, we investigate the structural and dynamical properties of the IL2RA promoter and identify an intrinsically negative supercoil in the PRRII region (containing Elf-1 and HMGA1 binding sites), located upstream of a curved DNA region encompassing TSS. Conformational changes, evidenced by time-lapse studies, result in the progressive positioning of curvature apex towards the TSS, likely facilitating local DNA melting. In vitro assays confirm specific binding of the General Transcription Factors (GTFs) TBP and TFIIB over TATA-TSS position, where an inhibitory nucleosome prevented preinitiation complex (PIC) formation and uncontrolled DNA melting. These findings represent a substantial advance showing, first, that the structural properties of the IL2RA promoter are encoded in the DNA sequence and second, that during the initiation process DNA conformation is dynamic and not static

Nucleosomes in gene regulation: theoretical approaches

This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from molecular-mechanistic and biological point of view. In addition to classical problems of this field, actual questions of epigenetic regulation are discussed. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field

Nucleosome positioning by genomic excluding-energy barriers

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Overexpression and Characterization of the Chromosomal Aminoglycoside 2′-N-Acetyltransferase of Providencia stuartii

The gene coding for aminoglycoside 2′-N-acetyltransferase Ia [AAC(2′)-Ia] from Providencia stuartii was amplified by PCR and cloned. The resulting construct, pACKF2, was transferred into Escherichia coli for overexpression of AAC(2′)-Ia as a fusion protein with an N-terminal hexa-His tag. The fusion protein was isolated and purified by affinity chromatography on Ni(2+)-nitrilotriacetic acid agarose and gel permeation chromatography on Superdex 75. Comparison of the specific activity of this enzyme with that of its enterokinase-digested derivative lacking the His tag indicated that the presence of the extra N-terminal peptide does not affect activity. The temperature and pH optima for activity of both forms of the 2′-N-acetyltransferase were 20°C and pH 6.0, respectively, while the enzymes were most stable at 15°C and pH 8.1. The Michaelis-Menten kinetic parameters for AAC(2′)-Ia at 20°C and pH 6.0 were determined using a series of aminoglycoside antibiotics possessing a 2′-amino group and a concentration of acetyl coenzyme A fixed at 10 times its K(m) value of 8.75 μM. Under these conditions, gentamicin was determined to be the best substrate for the enzyme in terms of both K(m) and k(cat)/K(m) values, whereas neomycin was the poorest. Comparison of the kinetic parameters obtained with the different aminoglycosides indicated that their hexopyranosyl residues provided the most important binding sites for AAC(2′)-Ia activity, while the enzyme exhibits greater tolerance further from these sites. No correlation was found between these kinetic parameters and MICs determined for P. stuartii PR50 expressing the 2′-N-acetyltransferase, suggesting that its true in vivo function is not as a resistance factor

Demographics and Baseline Characteristics of Patients with Idiopathic Pulmonary Fibrosis (IPF) in a Real-World Setting: Results of 847 Patients Enrolled in the Radico-ILD Cohort in France

International audienceRationale: Idiopathic pulmonary fibrosis (IPF) is a rare condition and few epidemiological dataare available in France. This specific research project aims to describe characteristics of treatedIPF patients and the impact of antifibrotic treatments in terms of morbidity and mortality in theFrench real-life setting. Methods: The French RaDiCo (Rare Disease Cohort)-ILD (idiopathicInterstitial Lung Diseases) registry is an ongoing observational study initiated in June 2017, witha sub-analysis of IPF patients. This longitudinal long-term cohort includes pediatric and adultpatients with ILD and is supported by the national network of reference and competence centersfor rare pulmonary diseases. IPF was diagnosed using international ATS/ERS 2011 criteria witha diagnosis of IPF or working diagnosis of IPF by multidisciplinary discussion. Here, we presentthe baseline data of IPF patients. Results: Between June 15th 2017 and September 4th 2019,1246 ILD patients were enrolled in the RaDiCo-ILD registry from 18 centers, including 847 withIPF (68%). IPF patients were mostly male (82.7%), with a mean age of 72.5 ± 9 years at inclusionand a mean BMI of 26.8 ± 4.3; 44.6 % of IPF patients included were incident cases, with amedian length between diagnosis and inclusion of 8.9 months (Q1=0.9 and Q3=26.4); 25.3% hada biopsy. The mean FVC at IPF diagnosis was 73.4 ± 25.0 % of predicted value (n=561), and themean DLCO at IPF diagnosis was 39.6 ± 18.2 % predicted value (n=498). Among patients withavailable information on anti-fibrotic treatment, 347 had been treated (at least one dose) withnintedanib, and 312 with pirfenidone; among patients treated with antifibrotics, 113 were treatedwith both treatments sequentially. Conclusions: The RaDiCo-ILD registry provides accurate real-world data on the demographics of patients with IPF in France. It will generate a long-term follow-up and will be an invaluable tool to describe the natural history and progression of patients withIPF in real-life conditions