One-carbon metabolism nutrients impact the interplay between DNA methylation and gene expression in liver, enhancing protein synthesis in Atlantic salmon.

Supplementation of one-carbon (1C) metabolism micronutrients, which include B-vitamins and methionine, is essential for the healthy growth and development of Atlantic salmon (Salmo salar). However, the recent shift towards non-fish meal diets in salmon aquaculture has led to the need for reassessments of recommended micronutrient levels. Despite the importance of 1C metabolism in growth performance and various cellular regulations, the molecular mechanisms affected by these dietary alterations are less understood. To investigate the molecular effect of 1C nutrients, we analysed gene expression and DNA methylation using two types of omics data: RNA sequencing (RNA-seq) and reduced-representation bisulphite sequencing (RRBS). We collected liver samples at the end of a feeding trial that lasted 220 days through the smoltification stage, where fish were fed three different levels of four key 1C nutrients: methionine, vitamin B6, B9, and B12. Our results indicate that the dosage of 1C nutrients significantly impacts genetic and epigenetic regulations in the liver of Atlantic salmon, particularly in biological pathways related to protein synthesis. The interplay between DNA methylation and gene expression in these pathways may play an important role in the mechanisms underlying growth performance affected by 1C metabolism.

Seasonal Changes in Photoperiod: Effects on Growth and Redox Signaling Patterns in Atlantic Salmon Postsmolts.

Farmed Atlantic salmon reared under natural seasonal changes in sea-cages had an elevated consumption of antioxidants during spring. It is, however, unclear if this response was caused by the increase in day length, temperature, or both. The present study examined redox processes in Atlantic salmon that were reared in indoor tanks at constant temperature (9 °C) under a simulated natural photoperiod. The experiment lasted for 6 months, from vernal to autumnal equinoxes, with the associated increase and subsequent decrease in day length. We found that intracellular antioxidants were depleted, and there was an increase in malondialdehyde (MDA) levels in the liver and muscle of Atlantic salmon with increasing day length. Antioxidant enzyme activity in liver and muscle and their related gene profiles was also affected, with a distinct upregulation of genes involved in maintaining redox homeostasis, such as peroxiredoxins in the brain in April. This study also revealed a nuclear factor-erythroid 2-related factor 2 (Nrf2)-mediated oxidative stress response in muscle and liver, suggesting that fish integrate environmental signals through redox signaling pathways. Furthermore, growth and expression profiles implicated in growth hormone (GH) signaling and cell cycle regulation coincided with stress patterns. The results demonstrate that a change in photoperiod without the concomitant increase in temperature is sufficient to stimulate growth and change the tissue oxidative state in Atlantic salmon during spring and early summer. These findings provide new insights into redox regulation mechanisms underlying the response to the changing photoperiod, and highlight a link between oxidative status and physiological function.

Long-term hemodynamic changes in cerebral proliferative angiopathy presenting with intracranial hemorrhage: illustrative case.

BACKGROUND: Cerebral proliferative angiopathy (CPA) is a rare vascular proliferative disease; however, long-term follow-up reports are scarce. The authors report a rare case and document a patient's medical history over 20 years. OBSERVATIONS: A 5-year-old girl developed left frontal lobe hemorrhage, presenting with headache. At 8 years of age, angiography showed diffuse capillary ectasia without an arteriovenous shunt. Single-photon emission computed tomography (SPECT) showed normal cerebral blood flow (CBF). She had normal growth without systemic disease. At 25 years of age, an intraventricular hemorrhage occurred, presenting with sudden headache. Angiography revealed vascular lesion enlargement, increased feeding arteries, dural supply to the nidus and peri-nidal lesion, and flow-related aneurysm. SPECT showed remarkable decreases in CBF in the nidus and peri-nidal lesion. Cerebral proliferative angiopathy (CPA) was diagnosed, and the aneurysm arising at the lateral posterior choroidal artery caused the hemorrhage. Coil embolization of the aneurysm was performed with a flow-guide catheter and extremely soft platinum coils. New aneurysms were not noted 1.5 years after the procedure. LESSONS: This is the first report to demonstrate hemodynamic changes in CPA on angiography and SPECT over 17 years. The development of endovascular devices has enabled the embolization of ruptured aneurysms at the peripheral cerebral artery.

Mechanistic study of Al2O3 coating effects on lithium deposition and dissolution reaction.

Lithium metal anodes show great promise for use in next-generation secondary batteries, but they suffer from lithium dendrite growth, as well as other issues, which cause safety problems and result in a loss of capacity with time. The use of artificial inorganic solid electrolyte interphase (SEI) layers, such as those comprising Al2O3, is a promising way to mitigate these disadvantages, but the mechanism behind these observed improvements remains poorly understood. Therefore, in this study, using pulsed laser deposition (PLD), the surface of a Cu electrode was coated with a physicochemically stable and mechanically strong Al2O3 thin film, and the effects of the film coating on the lithium deposition and dissolution behaviour were investigated. When the morphology of the deposits was evaluated by scanning electron microscopy, small lithium nuclei (approximately 0.2 µm in diameter) were observed to be deposited uniformly over the entire surface of the uncoated Cu electrode in the initial electrodeposition, and these grew into needle-like crystals from the nuclei. After 60 min of electrodeposition, the needle-like precipitates had aggregated and grown into three-dimensional structures with dendritic form. In contrast, on the surface of the Cu electrode modified with Al2O3 by PLD for 1 h, lithium clusters of about 50 µm in diameter were found to be aggregated and precipitated in the initial stages of electrodeposition. Notably, this is the first report of lithium deposition on Al2O3 thin films. With further cycling, the precipitates grew into two-dimensional flat plates. Analysis of the SEI film formed during the first deposition reaction revealed that the Al2O3 coating reduced the thickness of the SEI compared to that of the uncoated electrode. Therefore, the Al2O3 coating suppressed the decomposition of the electrolyte with the Cu electrode. The use of Al2O3 coatings results in (i) the growth of two-dimensional lithium clusters with an island shape on the Al2O3 thin film, and these could ensure a uniform electron conduction path to the electrode; in addition, (ii) the inhibited electrolyte decomposition caused by the low-surface-area lithium clusters and the low electronic conductivity of the Al2O3 thin film. These improve the coulombic efficiency and cycling behaviour.

Computational studies on defect chemistry and Li-ion conductivity of spinel-type LiAl5O8 as coating material for Li-metal electrode.

Li-metal rechargeable batteries are an attractive option for devices that require an extremely high specific energy density, high robustness, and long-term durability, such as high-altitude platform stations. However, Li dendrite growth during charge-discharge cycling causes short-circuit problems. One technical solution is to form an intermediate layer between the Li metal and electrolyte. This interfacial layer should possess mechanical strength, electrochemical stability in the presence of Li, and Li-ion conductivity. In this study, the Li-ion conductivity of spinel-type LiAl5O8 was investigated using first-principles density functional theory and force field molecular dynamics calculations. The calculation results confirmed that stoichiometric LiAl5O8 compounds do not exhibit Li-ion conductivity, whereas off-stoichiometric compounds with excess Li show long-range Li-ion diffusion. The evaluated activation energy was 0.28 eV, which is as low as that of well-known fast Li-ion conductors, such as garnet-type Li7La3Zr2O12. However, the extrapolated Li-ion conductivity at 298 K was relatively low (~ 10-6 S/cm) owing to the limited formation of migration pathways.

Impact of Antioxidant Feed and Growth Manipulation on the Redox Regulation of Atlantic Salmon Smolts.

Accumulating evidence indicates a close relationship between oxidative stress and growth rate in fish. However, the underlying mechanisms of this relationship remain unclear. This study evaluated the combined effect of dietary antioxidants and growth hormone (GH) on the liver and the muscle redox status of Atlantic salmon. There were two sequential experimental phases (EP) termed EP1 and EP2, each lasting for 6 weeks. In EP1, Atlantic salmon were fed either low-(L, 230 mg/kg ascorbic acid (Asc), 120 mg/kg α-tocopherol (α-TOH)), or high-(H, 380 mg/kg Asc, 210 mg/kg α-TOH)vitamin diets. The vitamins were supplemented as stable forms and the feeding was continued in EP2. In EP2, half of the fish were implanted with 3 µL per g body weight of recombinant bovine GH (Posilac®, 1 mg rbGH g BW-1) suspended in sesame oil, while the other half were held in different tanks and sham-implanted with similar volumes of the sesame oil vehicle. Here, we show that increasing high levels of vitamin C and E (diet H) increased their content in muscle and liver during EP1. GH implantation decreased vitamin C and E levels in both liver and muscle but increased malondialdehyde (MDA) levels only in the liver. GH also affected many genes and pathways of antioxidant enzymes and the redox balance. Among the most consistent were the upregulation of genes coding for the NADPH oxidase family (NOXs) and downregulation of the oxidative stress response transcription factor, nuclear factor-erythroid 2-related factor 2 (nrf2), and its downstream target genes in the liver. We verified that GH increases the growth rate until the end of the trail and induces an oxidative effect in the liver and muscle of Atlantic salmon. Dietary antioxidants do lower oxidative stress but have no effect on the growth rate. The present study is intended as a starting point to understand the potential interactions between growth and redox signaling in fish.

Micronutrient supplementation affects DNA methylation in male gonads with potential intergenerational epigenetic inheritance involving the embryonic development through glutamate receptor-associated genes.

BACKGROUND: DNA methylation has an important role in intergenerational inheritance. An increasing number of studies have reported evidence of germline inheritance of DNA methylation induced by nutritional signals in mammals. Vitamins and minerals as micronutrients contribute to growth performance in vertebrates, including Atlantic salmon (Salmo salar), and also have a role in epigenetics as environmental factors that alter DNA methylation status. It is important to understand whether micronutrients in the paternal diet can influence the offspring through alterations of DNA methylation signatures in male germ cells. RESULTS: Here, we show the effect of micronutrient supplementation on DNA methylation profiles in the male gonad through a whole life cycle feeding trial of Atlantic salmon fed three graded levels of micronutrient components. Our results strongly indicate that micronutrient supplementation affects the DNA methylation status of genes associated with cell signalling, synaptic signalling, and embryonic development. In particular, it substantially affects DNA methylation status in the promoter region of a glutamate receptor gene, glutamate receptor ionotropic, NMDA 3A-like (grin3a-like), when the fish are fed both medium and high doses of micronutrients. Furthermore, two transcription factors, histone deacetylase 2 (hdac2) and a zinc finger protein, bind to the hyper-methylated site in the grin3a-like promoter. An estimated function of hdac2 together with a zinc finger indicates that grin3a-like has a potential role in intergenerational epigenetic inheritance and the regulation of embryonic development affected by paternal diet. CONCLUSIONS: The present study demonstrates alterations of gene expression patterns and DNA methylation signatures in the male gonad when Atlantic salmon are fed different levels of micronutrients. Alterations of gene expression patterns are of great interest because the gonads are supposed to have limited metabolic activities compared to other organs, whereas alterations of DNA methylation signatures are of great importance in the field of nutritional epigenetics because the signatures affected by nutrition could be transferred to the next generation. We provide extensive data resources for future work in the context of potential intergenerational inheritance through the male germline.

Efficacy of Post-Dilatation during Carotid Artery Stenting for Unstable Plaque Using a Double-Layer Stent Evaluated by OFDI.

Objective: This study aimed to use optical frequency domain imaging (OFDI) to evaluate the efficacy of post-dilatation (PD) after stent placement for unstable plaques during carotid artery stenting (CAS) using a double-layer stent. Methods: Twelve unstable carotid plaque lesions diagnosed by MRI were evaluated using OFDI during CAS. The pre-procedural minimum lumen diameter was 1.6 ± 0.7 mm. Each lesion was pre-dilated with balloon catheters (diameter, 5.3 ± 0.5 mm), and a double-layer stent was deployed. PD was performed with balloon catheters of the same size as those used for pre-dilatation. Cross-sectional OFDI images within the stented segment were evaluated at 1-mm intervals for a 20-mm segment, including the most stenotic lesion. Slice rates for the presence of in-stent plaque protrusion (PP) and plaque between the double-layer lumen were calculated. Results: No procedural complications occurred with the use of an embolic protection device. Compared to after stent placement, slice rates for any PP (44 ± 19% to 62 ± 22%, P <0.05) and plaque between the double-layer lumen (79 ± 16% to 91 ± 34%, P <0.05) were significantly increased after PD; slice rates for >500 µm PP (7.5 ± 14% to 0%, P <0.05) were significantly decreased. Visible debris were captured in 50% of lesions. Conclusion: PD after double-layer carotid stent placement decreases in-stent large PP. Double-layer construction contributed to the prevention of large PP, as the PP may have been crushed into debris by PD.

Metabolic and molecular signatures of improved growth in Atlantic salmon (Salmo salar) fed surplus levels of methionine, folic acid, vitamin B6 and B12 throughout smoltification.

A moderate surplus of the one carbon (1C) nutrients methionine, folic acid, vitamin B6 and B12 above dietary recommendations for Atlantic salmon has shown to improve growth and reduce hepatosomatic index in the on-growing saltwater period when fed throughout smoltification. Metabolic properties and molecular mechanisms determining the improved growth are unexplored. Here, we investigate metabolic and transcriptional signatures in skeletal muscle taken before and after smoltification to acquire deeper insight into pathways and possible nutrient­gene interactions. A control feed (Ctrl) or 1C nutrient surplus feed (1C+) were fed to Atlantic salmon 6 weeks prior to smoltification until 3 months after saltwater transfer. Both metabolic and gene expression signatures revealed significant 1C nutrient-dependent changes already at pre-smolt, but differences intensified when analysing post-smolt muscle. Transcriptional differences revealed lower expression of genes related to translation, growth and amino acid metabolisation in post-smolt muscle when fed additional 1C nutrients. The 1C+ group showed less free amino acid and putrescine levels, and higher methionine and glutathione amounts in muscle. For Ctrl muscle, the overall metabolic profile suggests a lower amino acid utilisation for protein synthesis, and increased methionine metabolisation in polyamine and redox homoeostasis, whereas transcription changes are indicative of compensatory growth regulation at local tissue level. These findings point to fine-tuned nutrient­gene interactions fundamental for improved growth capacity through better amino acid utilisation for protein accretion when salmon was fed additional 1C nutrients throughout smoltification. It also highlights potential nutritional programming strategies on improved post-smolt growth through 1C+ supplementation before and throughout smoltification.

Micronutrient supplementation affects transcriptional and epigenetic regulation of lipid metabolism in a dose-dependent manner.

Micronutrients (vitamins and minerals) have been less well studied compared to macronutrients (fats, proteins, and carbohydrates) although they play important roles in growth, metabolism, and maintenance of tissues. Hence, there is growing interest to understand the influence of micronutrients across various aspects in nutritional research. In the last two decades, aquaculture feeds have been shifted to containing more plant-based materials to meet the increasing demand and maintain the sustainability in the industry. A recent whole life cycle feeding trial of Atlantic salmon (Salmo salar) with graded levels of micronutrient packages has concluded that the levels of several B-vitamins and microminerals need to be increased from the current recommendation levels for optimal growth and fish welfare when plant-based diets are used. Here, we show the effect of micronutrient supplementation on hepatic transcriptional and epigenetic regulation in a dose dependent manner. . Specifically, our aim is to reveal the mechanisms of altered cell metabolism, which results in improved growth performance by micronutrient surpluses, at gene expression and DNA methylation levels. Our results strongly indicate that micronutrient supplementation suppresses gene expression in lipid metabolism in a dose-dependent manner and broadly affects DNA methylation in cell-adhesion and cell-signalling. In particular, it increases DNA methylation levels on the acetyl-CoA carboxylase alpha promoter in a concentration-dependent manner, which further suggests that acetyl-CoA carboxylase alpha is an upstream epigenetic regulator controlling its downstream lipid biosynthesis activities. This study demonstrates a comprehensive analysis to reveal an important role of micronutrients in lipid metabolism through epigenetic control of gene expression.

Parental Selenium Nutrition Affects the One-Carbon Metabolism and the Hepatic DNA Methylation Pattern of Rainbow Trout (Oncorhynchus mykiss) in the Progeny.

Selenium is an essential micronutrient and its metabolism is closely linked to the methionine cycle and transsulfuration pathway. The present study evaluated the effect of two different selenium supplements in the diet of rainbow trout (Onchorhynchus mykiss) broodstock on the one-carbon metabolism and the hepatic DNA methylation pattern in the progeny. Offspring of three parental groups of rainbow trout, fed either a control diet (NC, basal Se level: 0.3 mg/kg) or a diet supplemented with sodium selenite (SS, 0.8 mg Se/kg) or hydroxy-selenomethionine (SO, 0.7 mg Se/kg), were collected at swim-up fry stage. Our findings suggest that parental selenium nutrition impacted the methionine cycle with lower free methionine and S-adenosylmethionine (SAM) and higher methionine synthase (mtr) mRNA levels in both selenium-supplemented treatments. DNA methylation profiling by reduced representation bisulfite sequencing (RRBS) identified differentially methylated cytosines (DMCs) in offspring livers. These DMCs were related to 6535 differentially methylated genes in SS:NC, 6890 in SO:NC and 7428 in SO:SS, respectively. Genes with the highest methylation difference relate, among others, to the neuronal or signal transmitting and immune system which represent potential targets for future studies.

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.

Neurosecretory protein GL induces fat accumulation in mice.

We recently discovered a novel gene encoding a small secretory protein, neurosecretory protein GL (NPGL), which stimulates feeding behavior in mice following acute administration. These findings suggest that dysregulation of NPGL contributes to obesity and metabolic disease. To explore this possibility, we investigated the impact of prolonged exposure to NPGL through 13 days of chronic intracerebroventricular (i.c.v.) infusion and examined feeding behavior, body composition, expressions of lipid metabolic factors, respiratory metabolism, locomotor activity, and food preference. Under standard chow diet, NPGL increased white adipose tissue (WAT) mass without affecting feeding behavior and body mass. In contrast, when fed a high-calorie diet, NPGL stimulated feeding behavior and increased body mass concomitant with marked fat accumulation. Quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis revealed that mRNA expressions for key enzymes and related factors involved in lipid metabolism were increased in WAT and liver. Likewise, analyses of respiratory metabolism and locomotor activity revealed that energy expenditure and locomotor activity were significantly decreased by NPGL. In contrast, selective feeding of macronutrients did not alter food preference in response to NPGL, although total calorie intake was increased. Immunohistochemical analysis revealed that NPGL-containing cells produce galanin, a neuropeptide that stimulates food intake. Taken together, these results provide further support for NPGL as a novel regulator of fat deposition through changes in energy intake and locomotor activity.

Neurosecretory Protein GL, a Hypothalamic Small Secretory Protein, Participates in Energy Homeostasis in Male Mice.

We have recently identified from the avian hypothalamus a complementary DNA encoding a small secretory protein termed neurosecretory protein GL (NPGL). In chicks, NPGL increases body weight gain without affecting food intake. A database search reveals that NPGL is conserved throughout vertebrates. However, the central distribution and functional role of NPGL remains to be elucidated in mammals. In this study, we identified the precursor complementary DNA encoding NPGL from the mouse hypothalamus. Quantitative reverse transcription polymerase chain reaction and morphological analyses revealed that NPGL precursor messenger RNA is robustly expressed in the mediobasal hypothalamus with NPGL neurons specifically localized to the lateroposterior part of the arcuate nucleus in the hypothalamus. NPGL-immunoreactive fibers were observed in close anatomical contact with pro-opiomelanocortin neurons in the rostral region of the arcuate nucleus. NPGL messenger RNA expression was elevated by 24-hour fasting and reduced by feeding of a high-fat diet for 5 weeks. Furthermore, intracerebroventricular injection of mature NPGL increased food intake, pointing to an important role in feeding. Taken together, these findings report on the distribution of NPGL in the mammalian brain and point to an important role for this neuropeptide in energy homeostasis.

Precrec: fast and accurate precision-recall and ROC curve calculations in R.

The precision-recall plot is more informative than the ROC plot when evaluating classifiers on imbalanced datasets, but fast and accurate curve calculation tools for precision-recall plots are currently not available. We have developed Precrec, an R library that aims to overcome this limitation of the plot. Our tool provides fast and accurate precision-recall calculations together with multiple functionalities that work efficiently under different conditions. AVAILABILITY AND IMPLEMENTATION: Precrec is licensed under GPL-3 and freely available from CRAN (https://cran.r-project.org/package=precrec). It is implemented in R with C ++. CONTACT: takaya.saito@ii.uib.noSupplementary information: Supplementary data are available at Bioinformatics online.

The precision-recall plot is more informative than the ROC plot when evaluating binary classifiers on imbalanced datasets.

Binary classifiers are routinely evaluated with performance measures such as sensitivity and specificity, and performance is frequently illustrated with Receiver Operating Characteristics (ROC) plots. Alternative measures such as positive predictive value (PPV) and the associated Precision/Recall (PRC) plots are used less frequently. Many bioinformatics studies develop and evaluate classifiers that are to be applied to strongly imbalanced datasets in which the number of negatives outweighs the number of positives significantly. While ROC plots are visually appealing and provide an overview of a classifier's performance across a wide range of specificities, one can ask whether ROC plots could be misleading when applied in imbalanced classification scenarios. We show here that the visual interpretability of ROC plots in the context of imbalanced datasets can be deceptive with respect to conclusions about the reliability of classification performance, owing to an intuitive but wrong interpretation of specificity. PRC plots, on the other hand, can provide the viewer with an accurate prediction of future classification performance due to the fact that they evaluate the fraction of true positives among positive predictions. Our findings have potential implications for the interpretation of a large number of studies that use ROC plots on imbalanced datasets.

MicroRNAs act complementarily to regulate disease-related mRNA modules in human diseases.

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.

Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments.

BACKGROUND: MicroRNA (miRNA) target genes tend to have relatively long and conserved 3' untranslated regions (UTRs), but to what degree these characteristics contribute to miRNA targeting is poorly understood. Different high-throughput experiments have, for example, shown that miRNAs preferentially regulate genes with both short and long 3' UTRs and that target site conservation is both important and irrelevant for miRNA targeting. RESULTS: We have analyzed several gene context-dependent features, including 3' UTR length, 3' UTR conservation, and messenger RNA (mRNA) expression levels, reported to have conflicting influence on miRNA regulation. By taking into account confounding factors such as technology-dependent experimental bias and competition between transfected and endogenous miRNAs, we show that two factors - target gene expression and competition - could explain most of the previously reported experimental differences. Moreover, we find that these and other target site-independent features explain about the same amount of variation in target gene expression as the target site-dependent features included in the TargetScan model. CONCLUSIONS: Our results show that it is important to consider confounding factors when interpreting miRNA high throughput experiments and urge special caution when using microarray data to compare average regulatory effects between groups of genes that have different average gene expression levels.

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.

MicroRNAs--targeting and target prediction.

MicroRNAs (miRNAs) are a class of small noncoding RNAs that can regulate many genes by base pairing to sites in mRNAs. The functionality of miRNAs overlaps that of short interfering RNAs (siRNAs), and many features of miRNA targeting have been revealed experimentally by studying miRNA-mimicking siRNAs. This review outlines the features associated with animal miRNA targeting and describes currently available prediction tools.