Dynamical DNA accessibility induced by chromatin remodeling and protein binding

International audienceChromatin remodeling factors are enzymes being able to alter locally chromatin structure at the nucleosomal level and they actively participate in the regulation of gene expression. Using simple rules for individual nucleosome motion induced by a remodeling factor, we designed simulations of the remodeling of oligomeric chromatin, in order to address quantitatively collective effects in DNA accessibility upon nucleosome mobilization. Our results suggest that accessibility profiles are inhomogeneous thanks to borders effects like protein binding. Remarkably, we show that the accessibility lifetime of DNA sequence is roughly doubled in the vicinity of borders as compared to its value in bulk regions far from the borders. These results are quantitatively interpreted as resulting from the confined diffusion of a large nucleosome depleted region

Characterization of the glass transition in vitreous silica by temperature scanning small-angle X-ray scattering

The temperature dependence of the x-ray scattering in the region below the first sharp diffraction peak was measured for silica glasses with low and high OH content (GE-124 and Corning 7980). Data were obtained upon scanning the temperature at 10, 40 and 80 K/min between 400 K and 1820 K. The measurements resolve, for the first time, the hysteresis between heating and cooling through the glass transition for silica glass, and the data have a better signal to noise ratio than previous light scattering and differential thermal analysis data. For the glass with the higher hydroxyl concentration the glass transition is broader and at a lower temperature. Fits of the data to the Adam-Gibbs-Fulcher equation provide updated kinetic parameters for this very strong glass. The temperature derivative of the observed X-ray scattering matches that of light scattering to within 14%.Comment: EurophysicsLetters, in pres

Chemical and dynamical processes in the mesospheric emissive layer. First results of stereoscopic observations

[1] The mesospheric emissive layer is an efficient tracer of the dynamical processes propagating in the atmosphere at that level. CCD images in the near infrared taken from the ground at slant angles often reveal the existence of wavy fields. A series of such images has been transformed, using matrix operations, producing a downward satellite-type view that covers a circular area of radius ∼1000 km at the altitude of the layer. The Fourier characteristics of the wave system are measured using a Morlet-type wavelet generator function with horizontal wavelengths of mostly ∼20–40 km and 100–150 km and temporal periods of ∼15–30 min. An oxygen-hydrogen model is used to evaluate the response of the emissive layer to a progressive density wave. The altitude of the layer is modulated with an amplitude of ∼0.8–1.8 km when a density wave propagates vertically. The layer thickness is slightly modulated and is equal to ∼7 km. Stereoscopic pairs of photographs taken simultaneously on 8–9 September 2000 at the Château-Renard and Pic du Midi observatories are used to obtain surface maps of the emission layer barycenter altitude. A stereocorrelation method suitable for low contrast objects without discrete contours is employed. Preliminary results for areas ∼50 × 50 km2 are presented. The surface maps of the layer barycenter altitude depict the existence of waves. They show the same wavy structure and compare favorably with the maps showing the emission intensity

Detection of circulating carcinoma cells by telomerase activity

Telomerase has been shown to be a marker of epithelial cancer cells. We developed a method that allows the detection of circulating carcinoma cells in the blood of cancer patients. Circulating epithelial cells are harvested from peripheral blood mononuclear cells by immunomagnetic separation using BerEP4-coated beads. A telomeric repeat amplification protocol (TRAP)-ELISA is then used to measure telomerase in harvested epithelial cells. This method is specific and sensitive as demonstrated by experiments using BerEP4-positive and negative cell lines. Whereas we never found telomerase activity in harvested epithelial cells (HEC) samples from 30/30 healthy donors, we have detected telomerase activity in HEC from 11/15 (73%) patients with stage IIIB or IV non-small cell lung cancer (NSCLC) patients and from 8/11 (72%) stage C or D (Dukes classification) colon cancer patients. This non-invasive method could be of great value as a diagnostic or prognostic marker, or for monitoring cancer progression. © 2001 Cancer Research Campaign http://www.bjcancer.co

Characterization of the poplar pan-genome by genome-wide identification of structural variation

Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa. We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2?Mb and 62.9?Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome