Rationale Misregulation of angiotensin II (Ang II) actions can lead to atherosclerosis and hypertension. Evaluating transcriptomic responses to Ang II in vascular smooth muscle cells (VSMCs) is important to understand the gene networks regulated by Ang II which might uncover previously unidentified mechanisms and new therapeutic targets. Objective To identify all transcripts, including novel protein-coding and long non-coding RNAs, differentially expressed in response to Ang II in rat VSMCs using transcriptome and epigenome profiling. Methods and Results De novo assembly of transcripts from RNA-seq revealed novel protein-coding and long non-coding RNAs (lncRNAs). The majority of the genomic loci of these novel transcripts are enriched for histone H3 lysine-4-trimethylation and histone H3 lysine-36-trimethylation, two chromatin modifications found at actively transcribed regions, providing further evidence that these are bonafide transcripts. Analysis of transcript abundance identified all protein-coding and lncRNAs regulated by Ang II. We further discovered that one Ang II-regulated lncRNA functions as the host transcript for miR-221 and miR-222, two miRNAs implicated in cell proliferation. Additionally, siRNA-mediated knockdown of Lnc-Ang362 reduced proliferation of VSMCs. Conclusions These data provide novel insights into the epigenomic and transcriptomic effects of Ang II in VSMCs. They provide the first identification of Ang II-regulated lncRNAs, which suggests functional roles for these lncRNAs in mediating cellular responses to Ang II. Furthermore, we identify one Ang IIregulated lncRNA that is responsible for the production of two miRNAs implicated in VSMC proliferation. These newly identified non-coding transcripts could be exploited as novel therapeutic targets for Ang II-associated cardiovascular diseases.

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Obesity is a highly heritable complex disease that results from the interaction of multiple genetic and environmental factors. Formerly obese individuals are susceptible to metabolic disorders later in life, even after lifestyle changes are made to mitigate the obese state. This is reminiscent of the metabolic memory phenomenon originally observed for persistent complications in diabetic patients, despite subsequent glycemic control. Epigenetic modifications represent a potential mediator of this observed memory. We previously demonstrated that a high fat diet leads to changes in chromatin accessibility in the mouse liver. The regions of greatest chromatin changes in accessibility are largely strain-dependent, indicating a genetic component in diet-induced chromatin alterations. We have now examined the persistence of diet-induced chromatin accessibility changes upon diet reversal in two strains of mice. We find that a substantial fraction of loci that undergo chromatin accessibility changes with a high fat diet remains in the remodeled state after diet reversal in C57BL/6J mice. In contrast, the vast majority of dietinduced chromatin accessibility changes in A/J mice are transient. Our data also indicate that the persistent chromatin accessibility changes observed in C57BL/6J mice are associated with specific transcription factors and histone post-translational modifications. The persistent loci identified here are likely to be contributing to the overall phenotype and are attractive targets for therapeutic intervention.Obesity and related metabolic diseases result from both genetic and environmental factors, such as exercise and diet. However, the molecular mechanisms that contribute to disease progression remain unclear. Intriguingly, previously obese individuals have increased mortality compared with normal individuals, despite therapeutic intervention (1). This is reminiscent of "metabolic memory," a phenomenon originally described in diabetic patients in which micro-and macrovascular complications develop long after blood glucose is normalized (2-4). It has been hypothesized that epigenetic modifications, such as alterations to the chromatin and non-sequence changes to DNA, including DNA methylation, can contribute to this "metabolic memory" (5-7).It is now well established that epigenetic modifications can contribute to disease progression (8). One manner by which external environmental factors can influence molecular pathways is through alterations to chromatin. It has been shown that high fat (HF) 2 diet leads to chromatin accessibility changes in the liver tissue of mice (9). Intriguingly, the genomic loci with the greatest degree of diet-induced chromatin accessibility changes are largely strain-specific, indicating a role for genetics in this response (9). Previous studies examining diet-induced metabolic dysfunctions have shown that mice that transition from HF to diets that are low in fats do not completely revert to the same state as mice only maintained on low fat diets (10). The data indicate th...

Investigations into the genomic landscape of histone modifications in heterochromatic regions have revealed histone H3 lysine 9 dimethylation (H3K9me2) to be important for differentiation and maintaining cell identity. H3K9me2 is associated with gene silencing and is organized into large repressive domains that exist in close proximity to active genes, indicating the importance of maintenance of proper domain structure. Here we show that nickel, a nonmutagenic environmental carcinogen, disrupted H3K9me2 domains, resulting in the spreading of H3K9me2 into active regions, which was associated with gene silencing. We found weak CCCTC-binding factor (CTCF)-binding sites and reduced CTCF binding at the Ni-disrupted H3K9me2 domain boundaries, suggesting a loss of CTCF-mediated insulation function as a potential reason for domain disruption and spreading. We furthermore show that euchromatin islands, local regions of active chromatin within large H3K9me2 domains, can protect genes from H3K9me2-spreadingassociated gene silencing. These results have major implications in understanding H3K9me2 dynamics and the consequences of chromatin domain disruption during pathogenesis.insulator | nickel toxicity | nickel carcinogenesis

BackgroundFunctional regulatory regions in eukaryotic genomes are characterized by the disruption of nucleosomes leading to accessible chromatin. The modulation of chromatin accessibility is one of the key mediators of transcriptional regulation, and variation in chromatin accessibility across individuals has been linked to complex traits and disease susceptibility. While mechanisms responsible for chromatin variation across individuals have been investigated, the overwhelming majority of chromatin variation remains unexplained. Furthermore, the processes through which the variation of chromatin accessibility contributes to phenotypic diversity remain poorly understood.ResultsWe profiled chromatin accessibility in liver from seven strains of mice with phenotypic diversity in response to a high-fat/high-sucrose (HF/HS) diet and identified reproducible chromatin variation across the individuals. We found that sites of variable chromatin accessibility were more likely to coincide with particular classes of transposable elements (TEs) than sites with common chromatin signatures. Evolutionarily younger long interspersed nuclear elements (LINEs) are particularly likely to harbor variable chromatin sites. These younger LINEs are enriched for binding sites of immune-associated transcription factors, whereas older LINEs are enriched for liver-specific transcription factors. Genomic region enrichment analysis indicates that variable chromatin sites at TEs may function to regulate liver metabolic pathways. CRISPR-Cas9 deletion of a number of variable chromatin sites at TEs altered expression of nearby metabolic genes. Finally, we show that polymorphism of TEs and differential DNA methylation at TEs can both influence chromatin variation.ConclusionsOur results demonstrate that specific classes of TEs show variable chromatin accessibility across strains of mice that display phenotypic diversity in response to a HF/HS diet. These results indicate that chromatin variation at TEs is an important contributor to phenotypic variation among populations.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0078-0) contains supplementary material, which is available to authorized users.