A two-step site and mRNA-level model for predicting microRNA targets

<p>Abstract</p> <p>Background</p> <p>Despite experiments showing that the number of microRNA (miRNA) target sites is critical for miRNA targeting, most existing methods focus on identifying individual miRNA target sites and do not model contributions of multiple target sites to miRNA regulation. To address this possible fault, we developed a miRNA target prediction model that recognizes the individual characteristics of functional binding sites and the global characteristics of miRNA-targeted mRNAs.</p> <p>Results</p> <p>Benchmark experiments showed that this two-step model generally had a higher overall performance than other established miRNA target prediction algorithms and that the model was especially suited to identify true miRNA targets among genes that all contain conserved target sites.</p> <p>Conclusions</p> <p>This improved performance could partly be explained by the model not relying on conservation when predicting targets. The critical factors for the model's performance, however, were mRNA-level features that characterized the number and strength of individual target sites within the mRNA. The model is available for online predictions or as pre-computed predictions on the human genome <url>http://tare.medisin.ntnu.no/mirna_target</url>.</p

Inferring causative variants in microRNA target sites

MicroRNAs (miRNAs) regulate genes post transcription by pairing with messenger RNA (mRNA). Variants such as single nucleotide polymorphisms (SNPs) in miRNA regulatory regions might result in altered protein levels and disease. Genome-wide association studies (GWAS) aim at identifying genomic regions that contain variants associated with disease, but lack tools for finding causative variants. We present a computational tool that can help identifying SNPs associated with diseases, by focusing on SNPs affecting miRNA-regulation of genes. The tool predicts the effects of SNPs in miRNA target sites and uses linkage disequilibrium to map these miRNA-related variants to SNPs of interest in GWAS. We compared our predicted SNP effects in miRNA target sites with measured SNP effects from allelic imbalance sequencing. Our predictions fit measured effects better than effects based on differences in free energy or differences of TargetScan context scores. We also used our tool to analyse data from published breast cancer and Parkinson's disease GWAS and significant trait-associated SNPs from the NHGRI GWAS Catalog. A database of predicted SNP effects is available at http://www.bigr.medisin.ntnu.no/mirsnpscore/. The database is based on haplotype data from the CEU HapMap population and miRNAs from miRBase 16.0

Intracellular trafficking of fatty acids in the fish intestinal epithelial cell line RTgutGC

The shift towards higher inclusion of vegetable oils (VOs) in aquafeeds has resulted in major changes in dietary fatty acid composition, especially increased amounts of monounsaturated fatty acids (MUFAs) and decreased polyunsaturated fatty acids (PUFAs) and saturated fatty acids (SFAs). However, little is known about how this change in fatty acid (FA) profile affects the intracellular fate of these fatty acids in the intestinal cells. To investigate this topic, we used the rainbow trout intestinal epithelial cell line (RTgutGC) as an in vitro model. The cells were incubated with either palmitic acid (16:0, PA), oleic acid (18:1n-9, OA), or arachidonic acid (20:4n-6, ARA), to represent the SFA, MUFA, and PUFA, respectively. In all experiments, the RTgutGC were incubated with either non-labeled or radiolabeled FA (PA, OA, or ARA) for 16 h at 190C. The cells were then analyzed for the occurrence of cytosolic lipid droplets (CLD) with confocal microscopy, transcriptomic analysis (non-labeled FA experiments) and lipid class composition in the cells and serosal media from the basolateral side of the cells (radiolabeled FA experiments). CLD accumulation was higher in RTgutGC exposed to OA compared to cells given PA or ARA. This was coupled with increased volume, diameter, and surface area of CLDs in OA treated cells than with other FAs (PA, ARA). The results from radiolabeled FAs performed on permeable transwell inserts showed that OA increased the triacylglycerides (TAG) synthesis and was primarily stored in the cells in CLDs; whereas a significant amount of ARA was transported as TAG to the basolateral compartment. A significant proportion of free FAs was found to be excreted to the serosal basolateral side by the cells, which was significantly higher for PA and OA than ARA. Although there were clear clusters in differentially expressed genes (DEGs) for each treatment group, results from transcriptomics did not correlate to lipid transport and CLD analysis. Overall, the accumulation of TAG in CLDs was higher for oleic acid (OA) compared to arachidonic acid (ARA) and palmitic acid (PA). To conclude, carbon chain length and saturation level of FA differently regulate their intracellular fate during fatty acid absorption.publishedVersio

Earlier or delayed seasonal broodstock spawning changes nutritional status and metabolic programming of growth for next-generation Atlantic salmon

Atlantic salmon (Salmo salar) breeding companies depend on changing light, temperature and feeding regimes to achieve new generations outside the natural spawning season. However, there have been few conducted trials reported that have studied whether this shift affects important traits. We test whether an induced shift of two months earlier or two months later than normal spawning season affects the nutritional status (folate, methionine, vitamin B12, vitamin B6, free amino acids, N-metabolites and lipids) in broodstock liver and muscle and whether this affects the levels of the same nutrients in the offspring. The results showed significant seasonal differences in the Cahill cycle (glucose-alanine cycle), 1C metabolism and for free amino acids catabolized in the citric acid cycle all which are important for embryonic growth The broodstock nutritional status was reflected in the eggs. Nutritional status of broodstock liver and muscle and newly fertilized eggs showed two general scenarios: Advanced spawning period did not obtain optimal deposition of nutrients in the eggs. Delayed spawning broodstock displayed a metabolic profile which indicated that it had enhanced catabolization of muscle protein which led to accumulation of aminogroups from muscle breakdown to such a degree that these amino groups were increased in the eggs. The total body weight at start-feeding stage revealed best growth for both the normal and late spawning compared to early spawning. We show here that environmental alterations in broodstock husbandry influence the nutrient status of the next generation via nutritional and metabolic programming. This is an important concept which needs more careful awareness as the metabolism compensate and regulate the energy between catabolism and anabolism through the early stages of cell divisions which give rise to changes in permanent traits for the next generation.publishedVersio

Out-of-season spawning affects the nutritional status and gene expression in both Atlantic salmon female broodstock and their offspring

The Atlantic salmon aquaculture industry relies on adjustments of female broodstock spawning season to meet the demand for delivery of embryos outside the natural spawning season. Earlier results from zebrafish have shown that parental micronutrient status program offspring metabolism. Therefore, the main hypothesis of this study was to investigate if out-of-season (off-season) broodstock (spawning in June, in land-based recirculation systems) and their offspring deviate in micronutrient status when compared to broodstock and offspring from normal spawning season. Both seasons of female Atlantic salmon broodstock were fed the same diet and starved for approximately the same time interval prior to spawning. We compared nutrients related to the 1C metabolism (vitamin B12, folate, vitamin B6, methionine), free amino acids (FAAs) and lipid classes in broodstock muscle and liver tissues, and during offspring ontogeny. In general, the off-season broodstock showed higher levels of folate, vitamin B6 and selected FAAs in muscle tissue, and higher levels of folate and lipids (cholesterol and sphingomyelin) in liver tissue compared to normal-season. Furthermore, embryos from off-season had reduced amounts of all the measured lipid classes, like cholesterol and sphingomyelin, and lower levels of one type of folate and changes in FAAs and N-metabolites. We discovered significant differences between the seasons in mRNA levels of genes controlling fatty acid synthesis and 1C metabolism in both broodstock liver and offspring. Moreover, for genes controlling the methylation of DNA; both maintenance and de novo DNA methyltransferases (DNMTs) were expressed at higher levels in off-season compared to normal-season offspring. Our results show, in general that normal spawning season broodstock allocated more nutrients to eggs than off-season. Our results indicate a potential for improved maturation for off-season group to obtain a higher offspring growth potential, and this argues for a reassessment of the nutritional influence from broodstock to offspring and the consequences through nutritional programming.publishedVersio

Journal Staff

MicroRNAs (miRNAs) play a key role in regulating mRNA expression, and individual miRNAs have been proposed as diagnostic and therapeutic candidates. The identification of such candidates is complicated by the involvement of multiple miRNAs and mRNAs as well as unknown disease topology of the miRNAs. Here, we investigated if disease-associated miRNAs regulate modules of disease-associated mRNAs, if those miRNAs act complementarily or synergistically, and if single or combinations of miRNAs can be targeted to alter module functions. We first analyzed publicly available miRNA and mRNA expression data for five different diseases. Integrated target prediction and network-based analysis showed that the miRNAs regulated modules of disease-relevant genes. Most of the miRNAs acted complementarily to regulate multiple mRNAs. To functionally test these findings, we repeated the analysis using our own miRNA and mRNA expression data from CD4+ T cells from patients with seasonal allergic rhinitis. This is a good model of complex diseases because of its well-defined phenotype and pathogenesis. Combined computational and functional studies confirmed that miRNAs mainly acted complementarily and that a combination of two complementary miRNAs, miR-223 and miR-139-3p, could be targeted to alter disease-relevant module functions, namely, the release of type 2 helper T-cell (Th2) cytokines. Taken together, our findings indicate that miRNAs act complementarily to regulate modules of disease-related mRNAs and can be targeted to alter disease-relevant functions