Epigenetic mechanisms and genome stability

Epigenetic marks are well recognized as heritable chemical modifications of DNA and chromatin that induce chromatin structural changes thereby affecting gene activity. A lesser-known phenomenon is the pervasive effects these marks have on genomic integrity. Remarkably, epigenetic marks and the enzymes that establish them are involved in multiple aspects of maintaining genetic content. These aspects include preserving nucleotide sequences such as repetitive elements, preventing DNA damage, functioning in DNA repair mechanisms and chromatin restoration, and defining chromosomal organization through effects on structural elements such as the centromere. This review discusses these functional aspects of epigenetic marks and their effects on human health and disease

Factors affecting accumulation of summer grass for winter standing feed in the high country

A 0.5 ha 6-year trial compared 6 grass species x 4 N fertiliser rates x 2 times of closing for summer-saved standing winter feed. The pre-winter yields averaged 3.4 t DM/ha from November, closing with a high browntop/sweet vernal component, as compared with 1.7 t DM/ha from December closings with a low browntop/sweet vernal component. Grasslands Kara cocksfoot was the highest yielding cultivar, followed by Grasslands Apanui cocksfoot, Grasslands Wana cocksfoot, Grasslands Roa tall fescue, Grasslands Nui perennial ryegrass and Grasslands Maru phalaris, with decreasing proportions of sown grass. Nitrogen fertiliser had a limited effect on prewinter yields but did have a carry-over effect into spring yields

DNA methylation age is accelerated in alcohol dependence.

Alcohol dependence (ALC) is a chronic, relapsing disorder that increases the burden of chronic disease and significantly contributes to numerous premature deaths each year. Previous research suggests that chronic, heavy alcohol consumption is associated with differential DNA methylation patterns. In addition, DNA methylation levels at certain CpG sites have been correlated with age. We used an epigenetic clock to investigate the potential role of excessive alcohol consumption in epigenetic aging. We explored this question in five independent cohorts, including DNA methylation data derived from datasets from blood (n = 129, n = 329), liver (n = 92, n = 49), and postmortem prefrontal cortex (n = 46). One blood dataset and one liver tissue dataset of individuals with ALC exhibited positive age acceleration (p < 0.0001 and p = 0.0069, respectively), whereas the other blood and liver tissue datasets both exhibited trends of positive age acceleration that were not significant (p = 0.83 and p = 0.57, respectively). Prefrontal cortex tissue exhibited a trend of negative age acceleration (p = 0.19). These results suggest that excessive alcohol consumption may be associated with epigenetic aging in a tissue-specific manner and warrants further investigation using multiple tissue samples from the same individuals

Reducing in-stent restenosis therapeutic manipulation of miRNA in vascular remodeling and inflammation

Background: Drug-eluting stents reduce the incidence of in-stent restenosis, but they result in delayed arterial healing and are associated with a chronic inflammatory response and hypersensitivity reactions. Identifying novel interventions to enhance wound healing and reduce the inflammatory response may improve long-term clinical outcomes. Micro–ribonucleic acids (miRNAs) are noncoding small ribonucleic acids that play a prominent role in the initiation and resolution of inflammation after vascular injury.<p></p> Objectives: This study sought to identify miRNA regulation and function after implantation of bare-metal and drug-eluting stents.<p></p> Methods: Pig, mouse, and in vitro models were used to investigate the role of miRNA in in-stent restenosis.<p></p> Results: We documented a subset of inflammatory miRNAs activated after stenting in pigs, including the miR-21 stem loop miRNAs. Genetic ablation of the miR-21 stem loop attenuated neointimal formation in mice post-stenting. This occurred via enhanced levels of anti-inflammatory M2 macrophages coupled with an impaired sensitivity of smooth muscle cells to respond to vascular activation.<p></p> Conclusions: MiR-21 plays a prominent role in promoting vascular inflammation and remodeling after stent injury. MiRNA-mediated modulation of the inflammatory response post-stenting may have therapeutic potential to accelerate wound healing and enhance the clinical efficacy of stenting

ON THE VORTEX BREAKDOWN PHENOMENON IN HIGH ANGLE OF ATTACK FLOWS OVER DELTA WING GEOMETRIES

ABSTRACT Using computational methods, an investigation was performed on the physical mechanisms leading to vortex breakdown in high angle of attack flows over delta wing geometries. For this purpose, the Second International Vortex Flow Experiment (VFE-2) 65° sweep delta wing model was studied at a root chord Reynolds number (Re cr ) of 6 × 10 6 at various angles of attack. The open-source computational fluid dynamics (CFD) solver OpenFOAM was used in parallel with the commercial CFD solver ANSYS® FLUENT. For breadth, a variety of classic closure models were applied, including unsteady Reynolds-averaged Navier-Stokes (URANS) and detached eddy simulation (DES). Results for all cases are analyzed and flow features are identified and discussed. The results show the inception of a pair of leading edge vortices originating at the apex for all models used, and a region of steady vortical structures downstream in the URANS results. However, DES results show regions of massively separated helical flow which manifests after vortex breakdown. Analysis of turbulence quantities in the breakdown region gives further insight into the mechanisms leading to such phenomena

Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells

BACKGROUND: The TET family of dioxygenases catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), but their involvement in establishing normal 5mC patterns during mammalian development and their contributions to aberrant control of 5mC during cellular transformation remain largely unknown. We depleted TET1, TET2, and TET3 in a pluripotent embryonic carcinoma cell model and examined the impact on genome-wide 5mC, 5hmC, and transcriptional patterns. RESULTS: TET1 depletion yields widespread reduction of 5hmC, while depletion of TET2 and TET3 reduces 5hmC at a subset of TET1 targets suggesting functional co-dependence. TET2 or TET3 depletion also causes increased 5hmC, suggesting these proteins play a major role in 5hmC removal. All TETs prevent hypermethylation throughout the genome, a finding dramatically illustrated in CpG island shores, where TET depletion results in prolific hypermethylation. Surprisingly, TETs also promote methylation, as hypomethylation was associated with 5hmC reduction. TET function is highly specific to chromatin environment: 5hmC maintenance by all TETs occurs at polycomb-marked chromatin and genes expressed at moderate levels; 5hmC removal by TET2 is associated with highly transcribed genes enriched for H3K4me3 and H3K36me3. Importantly, genes prone to hypermethylation in cancer become depleted of 5hmC with TET deficiency, suggesting that TETs normally promote 5hmC at these loci. Finally, all three TETs, but especially TET2, are required for 5hmC enrichment at enhancers, a condition necessary for expression of adjacent genes. CONCLUSIONS: These results provide novel insight into the division of labor among TET proteins and reveal important connections between TET activity, the chromatin landscape, and gene expression

Linking DNA Methyltransferases to Epigenetic Marks and Nucleosome Structure Genome-wide in Human Tumor Cells

DNA methylation, mediated by the combined action of three DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B), is essential for mammalian development and is a major contributor to cellular transformation. To elucidate how DNA methylation is targeted, we mapped the genome-wide localization of all DNMTs and methylation, and examined the relationships among these markers, histone modifications, and nucleosome structure in a pluripotent human tumor cell line in its undifferentiated and differentiated states. Our findings reveal a strong link between DNMTs and transcribed loci, and that DNA methylation is not a simple sum of DNMT localization patterns. A comparison of the epigenomes of normal and cancerous stem cells, and pluripotent and differentiated states shows that the presence of at least two DNMTs is strongly associated with loci targeted for DNA hypermethylation. Taken together, these results shed important light on the determinants of DNA methylation and how it may become disrupted in cancer cells.National Institutes of Health (U.S.) (Grant RC1HG005334)National Science Foundation (U.S.) (Postdoctoral Fellowship 0905968

Vinasse application and cessation of burning in sugarcane management can have positive impact on soil carbon stocks

Bioenergy crops, such as sugarcane, have the potential to mitigate greenhouse gas emissions through fossil fuel substitution. However, increased sugarcane propagation and recent management changes have raised concerns that these practices may deplete soil carbon (C) stocks, thereby limiting the net greenhouse gas benefit. In this study, we use both a measured and modelled approach to evaluate the impacts of two common sugarcane management practices on soil C sequestration potential in Brazil. We explore how transitions from conventional (mineral fertiliser/burning) to improved (vinasse application/unburned) practices influence soil C stocks in total and in physically fractionated soil down to one metre. Results suggest that vinasse application leads to an accumulation of soil C of 0.55 Mg ha−1yr−1 at 0–30 cm depth and applying unburned management led to gains of ∼0.7 Mg ha−1yr−1 at 30–60 cm depth. Soil C concentration in the Silt+Clay fraction of topsoil (0–20 cm) showed higher C content in unburned management but it did not differ under vinasse application. The CENTURY model was used to simulate the consequences of management changes beyond the temporal extent of the measurements. Simulations indicated that vinasse was not the key factor driving increases in soil C stocks but its application may be the most readily available practice to prevent the soil C losses under burned management. Furthermore, cessation of burning may increase topsoil C by 40% after ∼50 years. These are the first data comparing different sugarcane management transitions within a single area. Our findings indicate that both vinasse application and the cessation of burning can play an important role in reducing the time required for sugarcane ethanol production to reach a net C benefit (payback time)

Modulation of Dnmt3b function in vitro by interactions with Dnmt3L, Dnmt3a and Dnmt3b splice variants

DNA methylation, an essential regulator of transcription and chromatin structure, is established and maintained by the coordinated action of three DNA methyltransferases: DNMT1, DNMT3A and DNMT3B, and the inactive accessory factor DNMT3L. Disruptions in DNMT3B function are linked to carcinogenesis and genetic disease. DNMT3B is also highly alternatively spliced in a tissue- and disease-specific manner. The impact of intra-DNMT3 interactions and alternative splicing on the function of DNMT3 family members remains unclear. In the present work, we focused on DNMT3B. Using a panel of in vitro assays, we examined the consequences of DNMT3B splicing and mutations on its ability to bind DNA, interact with itself and other DNMT3's, and methylate DNA. Our results show that, while the C-terminal catalytic domain is critical for most DNMT3B functions, parts of the N-terminal region, including the PWWP domain, are also important. Alternative splicing and domain deletions also influence DNMT3B’s cellular localization. Furthermore, our data reveal the existence of extensive DNMT3B self-interactions that differentially impact on its activity. Finally, we show that catalytically inactive isoforms of DNMT3B are capable of modulating the activity of DNMT3A–DNMT3L complexes. Our studies therefore suggest that seemingly ‘inactive’ DNMT3B isoforms may influence genomic methylation patterns in vivo