Distinct Differences in Chromatin Structure at Subtelomeric X and Y' Elements in Budding Yeast

In Saccharomyces cerevisiae, all ends of telomeric DNA contain telomeric repeats of (TG1–3), but the number and position of subtelomeric X and Y' repeat elements vary. Using chromatin immunoprecipitation and genome-wide analyses, we here demonstrate that the subtelomeric X and Y' elements have distinct structural and functional properties. Y' elements are transcriptionally active and highly enriched in nucleosomes, whereas X elements are repressed and devoid of nucleosomes. In contrast to X elements, the Y' elements also lack the classical hallmarks of heterochromatin, such as high Sir3 and Rap1 occupancy as well as low levels of histone H4 lysine 16 acetylation. Our analyses suggest that the presence of X and Y' elements govern chromatin structure and transcription activity at individual chromosome ends

Silent but Not Static: Accelerated Base-Pair Substitution in Silenced Chromatin of Budding Yeasts

Subtelomeric DNA in budding yeasts, like metazoan heterochromatin, is gene poor, repetitive, transiently silenced, and highly dynamic. The rapid evolution of subtelomeric regions is commonly thought to arise from transposon activity and increased recombination between repetitive elements. However, we found evidence of an additional factor in this diversification. We observed a surprising level of nucleotide divergence in transcriptionally silenced regions in inter-species comparisons of Saccharomyces yeasts. Likewise, intra-species analysis of polymorphisms also revealed increased SNP frequencies in both intergenic and synonymous coding positions of silenced DNA. This analysis suggested that silenced DNA in Saccharomyces cerevisiae and closely related species had increased single base-pair substitution that was likely due to the effects of the silencing machinery on DNA replication or repair

Impact of Chromatin Structures on DNA Processing for Genomic Analyses

Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results of chromatin immunoprecipitation (ChIP) experiments. We initially discovered this effect at the Saccharomyces cerevisiae HMR locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. Using input samples from ChIP-Seq studies, we detected a similar bias throughout the heterochromatic portions of the yeast genome. We also observed significant chromatin-related effects at telomeres, protein binding sites, and genes, reflected in the variation of input-Seq coverage. Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects. Our results suggested that assays relying on immunoprecipitation of chromatin will be biased by intrinsic differences between regions packaged into different chromatin structures - biases which have been largely ignored to date. These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome

Histone H4 Lysine 12 Acetylation Regulates Telomeric Heterochromatin Plasticity in Saccharomyces cerevisiae

Recent studies have established that the highly condensed and transcriptionally silent heterochromatic domains in budding yeast are virtually dynamic structures. The underlying mechanisms for heterochromatin dynamics, however, remain obscure. In this study, we show that histones are dynamically acetylated on H4K12 at telomeric heterochromatin, and this acetylation regulates several of the dynamic telomere properties. Using a de novo heterochromatin formation assay, we surprisingly found that acetylated H4K12 survived the formation of telomeric heterochromatin. Consistently, the histone acetyltransferase complex NuA4 bound to silenced telomeric regions and acetylated H4K12. H4K12 acetylation prevented the over-accumulation of Sir proteins at telomeric heterochromatin and elimination of this acetylation caused defects in multiple telomere-related processes, including transcription, telomere replication, and recombination. Together, these data shed light on a potential histone acetylation mark within telomeric heterochromatin that contributes to telomere plasticity

Silent chromatin at the middle and ends: lessons from yeasts

Eukaryotic centromeres and telomeres are specialized chromosomal regions that share one common characteristic: their underlying DNA sequences are assembled into heritably repressed chromatin. Silent chromatin in budding and fission yeast is composed of fundamentally divergent proteins tat assemble very different chromatin structures. However, the ultimate behaviour of silent chromatin and the pathways that assemble it seem strikingly similar among Saccharomyces cerevisiae (S. cerevisiae), Schizosaccharomyces pombe (S. pombe) and other eukaryotes. Thus, studies in both yeasts have been instrumental in dissecting the mechanisms that establish and maintain silent chromatin in eukaryotes, contributing substantially to our understanding of epigenetic processes. In this review, we discuss current models for the generation of heterochromatic domains at centromeres and telomeres in the two yeast species

Fenton-like oxidation of reactive black 5 in the presence of LABO3 (B: Fe, Co, Mn, Ni) perovskite catalysts

The catalytic performances of LaBO3 (B: Fe, Co, Mn, Ni) perovskite catalysts in Fenton-like oxidation of the textile dye, Reactive Black 5 were compared, and, the optimum reaction conditions were investigated in the presence of the most efficient catalyst. Reactive Black 5 was selected as the model dye due to its complex chemical structure, high water solubility and common usage in the textile industry. The performances of the catalysts in Reactive Black 5 degradation and decolorization were compared by testing different catalyst loadings. According to the catalyst screening experiments, LaFeO3 showed the highest catalytic performance whereas LaCoO3, LaMnO3, and, LaNiO3 were not effective in the degradation and decolorization of Reactive Black 5. A parametric study was carried out in the presence of LaFeO3 catalyst in order to determine the most suitable reaction conditions. In the parametric study, the effect of catalyst loading, pH and the initial H2O2 concentration were investigated. The initial dye concentration and the reaction temperature were kept constant at 100 ppm and 50?, respectively. The most suitable reaction conditions were determined as 0.1 g/L of catalyst loading, 3 and 1 mM of H2O2, and, 96.9% degradation, and complete decolorization were achieved under these conditions. © 2018, Turkish Chemical Society. All rights reserved.15-MUH-030This study was supported by Ege University Scientific Research Project Fund [15-MUH-030]. -

Experimental study of the behavior of a steel-concrete hybrid thermal break system under vertical actions

International audienceThe level of energy performance requirements in buildings has substantially increased over the last twenty years. As a consequence, a large thickness of thermal insulation has to be used and the reduction of thermal bridges is necessary. This reduction becomes a main concern for structural design, particularly, at wall to balcony connections which cannot be left monolithic for concrete buildings with external thermal insulations in. For that kind of connections, a thermal break system (TBS) must be interleaved. The structural roles of this element are not only to transfer a vertical force and a bending moment but also to ensure the horizontal flexibility in order to absorb the relative displacements induced by thermal expansion of the balcony and to have a sufficient horizontal resistance for wind and seismic actions, where relevant. Moreover, this connection must answer to some minimal requirements of robustness. When considering all these aspects, the conventional TBS, made of stainless steel bars, appear to be inadequate. For that reason, a new solution of TBS, so-called SUNE, has been developed. It consists of tensioned rebars, U-shaped steel sections and special shear keys. In this article, the experimental tests to study the structural behavior of the SUNE under vertical actions are presented. An analytical formulation for determining the ultimate load of TBS and an analytical model for computing the flexural stiffness have been proposed and validated using the experimental results. © Springer International Publishing AG 2018

Experimental assessment of a hybrid process including adsorption/photo Fenton oxidation and microbial fuel cell for the removal of dicarboxylic acids from aqueous solution

In this study, the application of adsorption/photo Fenton oxidation and Microbial Fuel Cell was investigated for the degradation of dicarboxylic acids such as succinic acid and fumaric acid. The feasibility of a hybrid system combining an adsorption / photo Fenton-like oxidation and biological oxidation in a Microbial Fuel Cell (MFC) was investigated for the removal of succinic acid from aqueous solution. Adsorption and photo Fenton-like oxidation tests were carried out by using Fe-TiO2/AC (AC: Biomass derived activated carbon) as a catalyst. A removal of about 40.8 % was achieved in adsorption tests within 2 h at room temperature and 4 g/L of Fe-TiO2/AC loading. A slight improvement of the pollutant removal from the water phase was observed by the addition of an oxidant (H2O2) and the UV light source. The succinic acid solution was sent to a subsequent treatment in MFC: after 20 days a further removal of the pollutant of about 49.4 % with a mineralization of 35.5 % were observed. The adoption of a bioelectrochemical system allowed to convert the organics into electricity with a coulombic efficiency of 25.0 %. The biochemical oxidation of succinic acid and fumaric acid, the main product of the catalytic oxidation of succinic acid, was then carried out in a microbial fuel cell. A significant TOC reduction was achieved for both compounds, thus proving that they can be successfully used as electron source in microbial fuel cell treatment