Apelin-13 modulates the endometrial transcriptome of the domestic pig during implantation.

BACKGROUND: The peri-implantation period is a critical time during pregnancy that mostly defines the overall litter size. Most authors agree that the highest percentage of embryo mortality occurs during this time. Despite the brevity of the peri-implantation period, it is the most dynamic part of pregnancy in which the sequential and uninterrupted course of several processes is essential to the animal's reproductive success. Also then, the maternal uterine tissues undergo an intensive remodelling process, and their energy demand dramatically increases. It is believed that apelin, a member of the adipokine family, is involved in the control of female reproductive functions in response to the current metabolic state. The verified herein hypothesis assumed the modulatory effect of apelin on the endometrial tissue transcriptome on days 15 to 16 of gestation (beginning of implantation). RESULTS: The analysis of data obtained during RNA-seq (Illumina HiSeq2500) of endometrial slices treated and untreated with apelin (n = 4 per group) revealed changes in the expression of 68 genes (39 up-regulated and 29 down-regulated in the presence of apelin), assigned to 240 gene ontology terms. We also revealed changes in the frequency of alternative splicing events (397 cases), as well as single nucleotide variants (1,818 cases) in the presence of the adipokine. The identified genes were associated, among others, with the composition of the extracellular matrix, apoptosis, and angiogenesis. CONCLUSIONS: The obtained results indicate a potential role of apelin in the regulation of uterine tissue remodelling during the peri-implantation period.

The Carcinogenic Potential of Bisphenol A in the Liver Based on Transcriptomic Studies.

Bisphenol A (BPA) is an environmental toxin widely used in the production of polycarbonate plastics. A correlation exists between BPA tissue contamination and the occurrence of pathological conditions, including cancer. First-passage detoxification of high BPA amounts in the liver promotes hepatotoxicity and morphological alterations of this organ, but there is a lack of knowledge about the molecular mechanisms underlying these phenomena. This prompted us to investigate changes in the liver transcriptomics of 3-month-old female mice exposed to BPA (50 mg/kg) in drinking water for 3 months. Five female mice served as controls. The animals were euthanized, the livers were collected, and RNA was extracted to perform RNA-seq analysis. The multistep transcriptomic bioinformatics revealed 120 differentially expressed genes (DEGs) in the BPA-exposed samples. Gene Ontology (GO) annotations indicated that DEGs have been assigned to many biological processes, including "macromolecule modification" and "protein metabolic process". Several of the revealed DEGs have been linked to the pathogenesis of severe metabolic liver disorders and malignant tumors, in particular hepatocellular carcinoma. Data from this study suggest that BPA has a significant impact on gene expression in the liver, which is predictive of the carcinogenic potential of this compound in this organ.

Adaptation of the Porcine Pituitary Transcriptome, Spliceosome and Editome during Early Pregnancy.

The physiological mechanisms of the porcine reproduction are relatively well-known. However, transcriptomic changes and the mechanisms accompanying transcription and translation processes in various reproductive organs, as well as their dependence on hormonal status, are still poorly understood. The aim of this study was to gain a principal understanding of alterations within the transcriptome, spliceosome and editome occurring in the pituitary of the domestic pig (Sus scrofa domestica L.), which controls basic physiological processes in the reproductive system. In this investigation, we performed extensive analyses of data obtained by high-throughput sequencing of RNA from the gilts' pituitary anterior lobes during embryo implantation and the mid-luteal phase of the estrous cycle. During analyses, we obtained detailed information on expression changes of 147 genes and 43 long noncoding RNAs, observed 784 alternative splicing events and also found the occurrence of 8729 allele-specific expression sites and 122 RNA editing events. The expression profiles of the selected 16 phenomena were confirmed by PCR or qPCR techniques. As a final result of functional meta-analysis, we acquired knowledge regarding intracellular pathways that induce changes in the processes accompanying transcription and translation regulation, which may induce modifications in the secretory activity of the porcine adenohypophyseal cells.

Pulmonary artery embolism: comprehensive transcriptomic analysis in understanding the pathogenic mechanisms of the disease.

BACKGROUND: Pulmonary embolism (PE) is a severe disease that usually originates from deep vein thrombosis (DVT) of the lower extremities. This study set out to investigate the changes in the transcriptome of the pulmonary artery (PA) in the course of the PE in the porcine model. METHODS: The study was performed on 11 male pigs: a thrombus was formed in each right femoral vein in six animals, and then was released to induce PE, the remaining five animals served as a control group. In the experimental animals total RNA was isolated from the PA where the blood clot lodged, and in the control group, from the corresponding PA segments. High-throughput RNA sequencing was used to analyse the global changes in the transcriptome of PA with induced PE (PA-E). RESULTS: Applied multistep bioinformatics revealed 473 differentially expressed genes (DEGs): 198 upregulated and 275 downregulated. Functional Gene Ontology annotated 347 DEGs into 27 biological processes, 324 to the 11 cellular components and 346 to the 2 molecular functions categories. In the signaling pathway analysis, KEGG 'protein processing in endoplasmic reticulum' was identified for the mRNAs modulated during PE. The same KEGG pathway was also exposed by 8 differentially alternative splicing genes. Within single nucleotide variants, the 61 allele-specific expression variants were localised in the vicinity of the genes that belong to the cellular components of the 'endoplasmic reticulum'. The discovered allele-specific genes were also classified as signatures of the cardiovascular system. CONCLUSIONS: The findings of this research provide the first thorough investigation of the changes in the gene expression profile of PA affected by an embolus. Evidence from this study suggests that the disturbed homeostasis in the biosynthesis of proteins in the endoplasmic reticulum plays a major role in the pathogenesis of PE.

In Silico Identification of lncRNAs Regulating Sperm Motility in the Turkey (Meleagris gallopavo L.).

Long non-coding RNAs (lncRNAs) are transcripts not translated into proteins with a length of more than 200 bp. LncRNAs are considered an important factor in the regulation of countless biological processes, mainly through the regulation of gene expression and interactions with proteins. However, the detailed mechanism of interaction as well as functions of lncRNAs are still unclear and therefore constitute a serious research challenge. In this study, for the first time, potential mechanisms of lncRNA regulation of processes related to sperm motility in turkey were investigated and described. Customized bioinformatics analysis was used to detect and identify lncRNAs, and their correlations with differentially expressed genes and proteins were also investigated. Results revealed the expression of 863 new/unknown lncRNAs in ductus deferens, testes and epididymis of turkeys. Moreover, potential relationships of the lncRNAs with the coding mRNAs and their products were identified in turkey reproductive tissues. The results obtained from the OMICS study may be useful in describing and characterizing the way that lncRNAs regulate genes and proteins as well as signaling pathways related to sperm motility.

PPARγ regulates the expression of genes involved in the DNA damage response in an inflamed endometrium.

Inflammation is a biological response of the immune system, which can be triggered by many factors, including pathogens. These factors may induce acute or chronic inflammation in various organs, including the reproductive system, leading to tissue damage or disease. In this study, the RNA-Seq technique was used to determine the in vitro effects of peroxisome proliferator-activated receptor gamma (PPARγ) ligands on the expression of genes and long non-coding RNA, and alternative splicing events (ASEs) in LPS-induced inflammation of the porcine endometrium during the follicular phase of the estrous cycle. Endometrial slices were incubated in the presence of LPS and PPARγ agonists (PGJ2 or pioglitazone) and a PPARγ antagonist (T0070907). We identified 169, 200, 599 and 557 differentially expressed genes after LPS, PGJ2, pioglitazone or T0070907 treatment, respectively. Moreover, changes in differentially expressed long non-coding RNA and differential alternative splicing events were described after the treatments. The study revealed that PPARγ ligands influence the LPS-triggered expression of genes controlling the DNA damage response (GADD45ß, CDK1, CCNA1, CCNG1, ATM). Pioglitazone treatment exerted a considerable effect on the expression of genes regulating the DNA damage response.

Chemerin Impact on Alternative mRNA Transcription in the Porcine Luteal Cells.

Chemerin participates in the regulation of processes related to physiological and disorder mechanisms in mammals, including metabolism, obesity, inflammation, and reproduction. In this study, we have investigated chemerin influence on alternative mRNA transcription within the porcine luteal cell transcriptome, such as differential expression of long non-coding RNAs (DELs) and their interactions with differentially expressed genes (DEGs), differences in alternative splicing of transcripts (DASs), and allele-specific expression (ASEs) related to the single nucleotide variants (SNVs) frequency. Luteal cells were collected from gilts during the mid-luteal phase of the oestrous cycle. After in vitro culture of cells un-/treated with chemerin, the total RNA was isolated and sequenced using the high-throughput method. The in silico analyses revealed 24 DELs cis interacting with 6 DEGs and trans-correlated with 300 DEGs, 137 DASs events, and 18 ASEs. The results enabled us to analyse metabolic and signalling pathways in detail, providing new insights into the effects of chemerin on the corpus luteum functions related to inflammatory response, leukocyte infiltration, the occurrence of luteotropic and luteolytic signals (leading to apoptosis and/or necroptosis). Validation of the results using qPCR confirmed the predicted expression changes. Chemerin at physiological concentrations significantly modifies the transcription processes in the porcine luteal cells.

Transcription Analysis of the Chemerin Impact on Gene Expression Profile in the Luteal Cells of Gilts.

Chemerin is a recently discovered adipokine that participates in the regulation of many physiological and disorder-related processes in mammals, including metabolism, inflammatory reactions, obesity, and reproduction. We investigated how chemerin affects the transcriptome profile of porcine luteal cells. The luteal cells were acquired from mature gilts. After the in vitro culturing with and without chemerin, the total RNAs were isolated and high-throughput sequencing was performed. Obtained datasets were processed using bioinformatic tools. The study revealed 509 differentially expressed genes under the chemerin influence. Their products take part in many processes, important for the functions of the corpus luteum, such as steroids and prostaglandins synthesis, NF-κB and JAK/STAT signal transducing pathways, and apoptosis. The expression of the CASP3, HSD3B7, IL1B, and PTGS2 genes, due to their important role in the physiology of the corpus luteum, was validated using the quantitative real-time polymerase chain reaction (qPCR) method. The qPCR confirmed the changes of gene expression. Chemerin in physiological concentrations significantly affects the expression of many genes in luteal cells of pigs, which is likely to result in modification of physiological processes related to reproduction.

Author Correction: Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta.

Despite the use of Hymenolepis diminuta as a model organism in experimental parasitology, a full genome description has not yet been published. Here we present a hybrid de novo genome assembly based on complementary sequencing technologies and methods. The combination of Illumina paired-end, Illumina mate-pair and Oxford Nanopore Technology reads greatly improved the assembly of the H. diminuta genome. Our results indicate that the hybrid sequencing approach is the method of choice for obtaining high-quality data. The final genome assembly is 177 Mbp with contig N50 size of 75 kbp and a scaffold N50 size of 2.3 Mbp. We obtained one of the most complete cestode genome assemblies and annotated 15,169 potential protein-coding genes. The obtained data may help explain cestode gene function and better clarify the evolution of its gene families, and thus the adaptive features evolved during millennia of co-evolution with their hosts.