Identification Of Potential Regulators Research Articles

Abstract 12461: Identification of Differentially Expressed Long Non-Coding RNAs in Human-Induced Pluripotent Stem Cell-Derived Endothelial Cells Triggered by E-cigarette Exposure

Introduction: Electronic-cigarette (e-cig) usage, particularly in the youth population, is a growing concern. It is known that e-cig causes endothelial dysfunction, which is a risk factor for the development of cardiovascular diseases; however, the mechanisms involved remain unclear. We hypothesized that long non-coding RNAs (lncRNAs), a novel class of non-coding RNA that has been shown to affect endothelial function, may play a role in e-cig-induced endothelial dysfunction. Methods and Results: We profiled lncRNAs that are dysregulated in human induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) from healthy individuals following 24 hours of e-cig aerosol extract treatment. Using microarray analysis, we identified that 183 lncRNAs and 132 mRNAs were upregulated while 297 lncRNAs and 413 mRNAs were downregulated. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analyses of the mRNAs dysregulated by e-cig exposure followed by the functional characterization of the top 5 differentially expressed (DE) lncRNAs by co-expressed protein-coding genes analysis. Interestingly, the lncRNA-mRNA association analysis revealed several mRNAs associated with metabolic disorders. Subsequently, we found that e-cig caused dysregulation of endothelial metabolism resulting in increased fatty acid oxidation activity, higher mitochondrial membrane potential, and decreased glucose uptake and glycolysis. These results suggest that e-cig-induced altered EC metabolism and increased fatty acid oxidation compensate for energy deficiency in ECs. Conclusion: Collectively, the identification of potential regulators and pathways of the interaction between lncRNAs and mRNAs in ECs treated with e-cig provides novel insights into endothelial biology and could have a significant impact on our understanding of vascular complications upon e-cig exposure.

Muscle Transcriptome Analysis Reveals Molecular Pathways Related to Oxidative Phosphorylation, Antioxidant Defense, Fatness and Growth in Mangalitsa and Moravka Pigs.

Simple SummaryThe study of gene expression at the transcriptome level provides rich information on the genes and metabolic pathways influencing relevant phenotypic traits. This study deals with the comparison of muscle transcriptome between two autochthonous pig breeds from Serbia (Mangalitsa and Moravka) as well as between Mangalitsa pigs fed a tannin-supplemented diet vs. a control one. The results provide a wide characterization of genes, pathways and potential regulatory mechanisms affecting muscle traits which differ among the experimental groups. The generated information improves the scientific knowledge on the cellular and metabolic basis of muscle growth, oxidative stability and fatness in pigs, and provides abundant candidate genes which could be responsible for phenotypic variation, and could be useful in future studies and selection approaches.This work was aimed at evaluating loin transcriptome and metabolic pathway differences between the two main Serbian local pig breeds with divergent characteristics regarding muscle growth and fatness, as well as exploring nutrigenomic effects of tannin supplementation in Mangalitsa (MA) pigs. The study comprised 24 Mangalitsa and 10 Moravka (MO) males, which were kept under identical management conditions. Mangalitsa animals were divided in two nutritional groups (n = 12) receiving a standard (control) or tannin–supplemented diet (1.5%; MAT). Moravka pigs were fed the standard mixture. All animals were slaughtered at a similar age; 120 kg of average live weight (LW) and loin tissue was used for RNA-seq analysis. Results showed 306 differentially expressed genes (DEGs) according to breed, enriched in genes involved in growth, lipid metabolism, protein metabolism and muscle development, such as PDK4, FABP4, MYOD1 and STAT3, as well as a relevant number of genes involved in mitochondrial respiratory activity (MT-NDs, NDUFAs among others). Oxidative phosphorylation was the most significantly affected pathway, activated in Mangalitsa muscle, revealing the basis of a different muscle metabolism. Also, many other relevant pathways were affected by breed and involved in oxidative stress response, fat accumulation and development of skeletal muscle. Results also allowed the identification of potential regulators and causal networks such as those controlled by FLCN, PPARGC1A or PRKAB1 with relevant regulatory roles on DEGs involved in mitochondrial and lipid metabolism, or IL3 and TRAF2 potentially controlling DEGs involved in muscle development. The Tannin effect on transcriptome was small, with only 23 DEGs, but included interesting ones involved in lipid deposition such as PPARGC1B. The results indicate a significant effect of the breed on muscle tissue gene expression, affecting relevant biological pathways and allowing the identification of strong regulatory candidate genes to underlie the gene expression and phenotypic differences between the compared groups.

Genome-wide role of codon usage on transcription and identification of potential regulators

Codon usage bias is a fundamental feature of all genomes and plays an important role in determining gene expression levels. The codon usage was thought to influence gene expression mainly due to its impact on translation. Recently, however, codon usage was shown to affect transcription of fungal and mammalian genes, indicating the existence of a gene regulatory phenomenon with unknown mechanism. In Neurospora, codon usage biases strongly correlate with mRNA levels genome-wide, and here we show that the correlation between codon usage and RNA levels is maintained in the nucleus. In addition, codon optimality is tightly correlated with both total and nuclear RNA levels, suggesting that codon usage broadly influences mRNA levels through transcription in a translation-independent manner. A large-scale RNA sequencing-based genetic screen in Neurospora identified 18 candidate factors that when deleted decreased the genome-wide correlation between codon usage and RNA levels and reduced the codon usage effect on gene expression. Most of these factors, such as the H3K36 methyltransferase, are chromatin regulators or transcription factors. Together, our results suggest that the transcriptional effect of codon usage is mediated by multiple transcriptional regulatory mechanisms.

Breed, Diet, and Interaction Effects on Adipose Tissue Transcriptome in Iberian and Duroc Pigs Fed Different Energy Sources.

In this study, we analyzed the effects of breed, diet energy source, and their interaction on adipose tissue transcriptome in growing Iberian and Duroc pigs. The study comprised 29 Iberian and 19 Duroc males, which were kept under identical management conditions except the nutritional treatment. Two isoenergetic diets were used with 6% high oleic sunflower oil (HO) or carbohydrates (CH) as energy sources. All animals were slaughtered after 47 days of treatment at an average live weight of 51.2 kg. Twelve animals from each breed (six fed each diet) were employed for ham subcutaneous adipose tissue RNA-Seq analysis. The data analysis was performed using two different bioinformatic pipelines. We detected 837 and 1456 differentially expressed genes (DEGs) according to breed, depending on the pipeline. Due to the strong effect of breed on transcriptome, the effect of the diet was separately evaluated in the two breeds. We identified 207 and 57 DEGs depending on diet in Iberian and Duroc pigs, respectively. A joint analysis of both effects allowed the detection of some breed–diet interactions on transcriptome, which were inferred from RNA-Seq and quantitative PCR data. The functional analysis showed the enrichment of functions related to growth and tissue development, inflammatory response, immune cell trafficking, and carbohydrate and lipid metabolism, and allowed the identification of potential regulators. The results indicate different effects of diet on adipose tissue gene expression between breeds, affecting relevant biological pathways.

13-P075 Genome-wide in vivo screening and identification of potential regulators of FGF signaling in Xenopus laevis system

13-P075 Genome-wide in vivo screening and identification of potential regulators of FGF signaling in Xenopus laevis system