Identification of reproduction-related gene polymorphisms using whole transcriptome sequencing in the Large White pig population

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Transcriptome profiling of the murine testis during the first wave of spermatogenesis

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Changes in gene expression linked with adult reproductive diapause in a northern malt fly species: a candidate gene microarray study

<p>Abstract</p> <p>Background</p> <p>Insect diapause is an important biological process which involves many life-history parameters important for survival and reproductive fitness at both individual and population level. <it>Drosophila montana</it>, a species of <it>D. virilis </it>group, has a profound photoperiodic reproductive diapause that enables the adult flies to survive through the harsh winter conditions of high latitudes and altitudes. We created a custom-made microarray for <it>D. montana </it>with 101 genes known to affect traits important in diapause, photoperiodism, reproductive behaviour, circadian clock and stress tolerance in model Drosophila species. This array gave us a chance to filter out genes showing expression changes during photoperiodic reproductive diapause in a species adapted to live in northern latitudes with high seasonal changes in environmental conditions.</p> <p>Results</p> <p>Comparisons among diapausing, reproducing and young <it>D. montana </it>females revealed expression changes in 24 genes on microarray; for example in comparison between diapausing and reproducing females one gene (<it>Drosophila cold acclimation gene, Dca</it>) showed up-regulation and 15 genes showed down-regulation in diapausing females. Down-regulation of seven of these genes was specific to diapause state while in five genes the expression changes were linked with the age of the females rather than with their reproductive status. Also, qRT-PCR experiments confirmed <it>couch potato </it>(<it>cpo</it>) gene to be involved in diapause of <it>D. montana</it>.</p> <p>Conclusions</p> <p>A candidate gene microarray proved to offer a practical and cost-effective way to trace genes that are likely to play an important role in photoperiodic reproductive diapause and further in adaptation to seasonally varying environmental conditions. The present study revealed two genes, <it>Dca </it>and <it>cpo</it>, whose role in photoperiodic diapause in <it>D. montana </it>is worth of studying in more details. Also, further studies using the candidate gene microarray with more specific experimental designs and target tissues may reveal additional genes with more restricted expression patterns.</p

Simvastatin Modulates Extracellular Matrix Assembly by Displaying an Antifibrotic Activity in Vitro

Statins, competitive inhibitors of 3-hydroxy-3-methylglutaryl coenzyme A reductase, are known to possess properties beyond their cholesterol-lowering effect including anti-inflammatory, antiproliferative and anti-immunomodulatory effects. We examined the effect of simvastatin on extracellular matrix (ECM) assembly by human skin fibroblasts (HSFs) in vitro. Using collagen gel contraction (CGC) assay we showed that simvastatin inhibits contraction of type I collagen-rich gels in a dose-dependent manner. This effect of simvastatin could be overcome by co-incubating the cells with mevalonate. Actin staining revealed that inhibition of CGC by simvastatin is associated with diminished ability of the cells to form aggregates. Using whole human genome Illumina microarray we sought to search for new candidate genes whose expression is regulated by simvastatin during CGC and focused specifically on the genes related to ECM synthesis and remodeling. We found that simvastatin profoundly downregulated gene expression of 27 ECM molecules including proteoglycans decorin and versican, both of which are known to be essential constituents of proper ECM. Expression of these two molecules was further verified by Northern blot analysis. Finally, when simvastatin treated HSFs were activated with TGF-β1, the cell-mediated contraction of collagen gel was restored. Our results indicate that simvastatin markedly alters ECM assembly in vitro possessing an antifibrotic activity.</p

Exon-level estimates improve the detection of differentially expressed genes in RNA-seq studies

Detection of differentially expressed genes (DEGs) between different biological conditions is a key data analysis step of most RNA-sequencing studies. Conventionally, computational tools have used gene-level read counts as input to test for differential gene expression between sample condition groups. Recently, it has been suggested that statistical testing could be performed with increased power at a lower feature level prior to aggregating the results to the gene level. In this study, we systematically compared the performance of calling the DEGs when using read count data at different levels (gene, transcript, and exon) as input, in the context of two publicly available data sets. Additionally, we tested two different methods for aggregating the lower feature-level p-values to gene-level: Lancaster and empirical Brown's method. Our results show that detection of DEGs is improved compared to the conventional gene-level approach regardless of the lower feature-level used for statistical testing. The overall best balance between accuracy and false discovery rate was obtained using the exon-level approach with empirical Brown's aggregation method, which we provide as a freely available Bioconductor package EBSEA (https://bioconductor.org/packages/release/bioc/html/EBSEA.html)

The impact of probiotic supplementation during pregnancy on DNA methylation of obesity-related genes in mothers and their children

PurposeDietary supplementation with probiotics during pregnancy has been suggested to decrease the risk for obesity in women after delivery and to minimize excessive weight gain in their children. Epigenetic DNA methylation has been proposed to impact on gene activity, thereby providing a plausible molecular mechanism for a broad range of biological processes and diseases. This pilot study aimed to evaluate whether probiotic supplementation during pregnancy could modify the DNA methylation status of the promoters of obesity and weight gain-related genes in mothers and their children.MethodsA sample of 15 pregnant women was taken from a prospective, randomized mother and infant nutrition and probiotic study. Seven women received the probiotic supplementation and eight served as controls. The women’s and their children’s DNA methylation status of obesity (623 genes) and weight gain-related (433) gene promoters were analyzed from blood samples at the mean of 9.8 months (range 6.1–12.7 months) postpartum.ResultsProbiotic supplementation led to significantly decreased levels of DNA methylation in 37 gene promoters and increased levels of DNA methylation in one gene promoter in women. In their children, 68 gene promoters were significantly affected consistently with a lower level of DNA methylation in the probiotic group.ConclusionsOn the basis of our pilot study, we suggest that probiotic supplementation during pregnancy may affect the DNA methylation status of certain promoters of obesity and weight gain-related genes both in mothers and their children, thereby providing a potential mechanism for long-lasting health effects.</div

Gene expression profiles and signaling mechanisms in α2B-adrenoceptor-evoked proliferation of vascular smooth muscle cells

Background: alpha(2)-adrenoceptors are important regulators of vascular tone and blood pressure. Regulation of cell proliferation is a less well investigated consequence of alpha(2)-adrenoceptor activation. We have previously shown that alpha B-2-adrenoceptor activation stimulates proliferation of vascular smooth muscle cells (VSMCs). This may be important for blood vessel development and plasticity and for the pathology and therapeutics of cardiovascular disorders. The underlying cellular mechanisms have remained mostly unknown. This study explored pathways of regulation of gene expression and intracellular signaling related to alpha B-2-adrenoceptor-evoked VSMC proliferation.Results: The cellular mechanisms and signaling pathways of alpha B-2-adrenoceptor-evoked proliferation of VSMCs are complex and include redundancy. Functional enrichment analysis and pathway analysis identified differentially expressed genes associated with alpha B-2-adrenoceptor-regulated VSMC proliferation. They included the upregulated genes Egr1, F3, Ptgs2 and Serpine1 and the downregulated genes Cx3cl1, Cav1, Rhoa, Nppb and Prrx1. The most highly upregulated gene, Lypd8, represents a novel finding in the VSMC context. Inhibitor library screening and kinase activity profiling were applied to identify kinases in the involved signaling pathways. Putative upstream kinases identified by two different screens included PKC, Raf-1, Src, the MAP kinases p38 and JNK and the receptor tyrosine kinases EGFR and HGF/HGFR. As a novel finding, the Src family kinase Lyn was also identified as a putative upstream kinase.Conclusions: alpha B-2-adrenoceptors may mediate their pro-proliferative effects in VSMCs by promoting the activity of bFGF and PDGF and the growth factor receptors EGFR, HGFR and VEGFR-1/2. The Src family kinase Lyn was also identified as a putative upstream kinase. Lyn is known to be expressed in VSMCs and has been identified as an important regulator of GPCR trafficking and GPCR effects on cell proliferation. Identified Ser/Thr kinases included several PKC isoforms and the beta-adrenoceptor kinases 1 and 2. Cross-talk between the signaling mechanisms involved in alpha(2) B-adrenoceptor-evoked VSMC proliferation thus appears to involve PKC activation, subsequent changes in gene expression, transactivation of EGFR, and modulation of kinase activities and growth factormediated signaling. While many of the identified individual signals were relatively small in terms of effect size, many of them were validated by combining pathway analysis and our integrated screening approach

Reproducibility-optimized detection of differential DNA methylation

Compared with state-of-the-art methods, ROTS shows competitive sensitivity and specificity in detecting consistently differentially methylated regions

Urine microRNA Profiling Displays miR-125a Dysregulation in Children with Fragile X Syndrome

A triplet repeat expansion leading to transcriptional silencing of the FMR1 gene results in fragile X syndrome (FXS), which is a common cause of inherited intellectual disability and autism. Phenotypic variation requires personalized treatment approaches and hampers clinical trials in FXS. We searched for microRNA (miRNA) biomarkers for FXS using deep sequencing of urine and identified 28 differentially regulated miRNAs when 219 reliably identified miRNAs were compared in dizygotic twin boys who shared the same environment, but one had an FXS full mutation, and the other carried a premutation allele. The largest increase was found in miR-125a in the FXS sample, and the miR-125a levels were increased in two independent sets of urine samples from a total of 19 FXS children. Urine miR-125a levels appeared to increase with age in control subjects, but varied widely in FXS subjects. Should the results be generalized, it could suggest that two FXS subgroups existed. Predicted gene targets of the differentially regulated miRNAs are involved in molecular pathways that regulate developmental processes, homeostasis, and neuronal function. Regulation of miR-125a has been associated with type I metabotropic glutamate receptor signaling (mGluR), which has been explored as a treatment target for FXS, reinforcing the possibility that urine miR-125a may provide a novel biomarker for FXS