Abstract
BackgroundLong non-coding RNAs (lncRNAs) may regulate gene expression in numerous biological processes including cellular response to xenobiotics. The exposure of living organisms to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a persistent environmental contaminant, results in reproductive defects in many species including pigs. The aims of the study were to identify and characterize lncRNAs in porcine granulosa cells as well as to examine the effects of TCDD on the lncRNA expression profile in the cells.ResultsOne thousand six hundred sixty-six lncRNAs were identified and characterized in porcine granulosa cells. The identified lncRNAs were found to be shorter than mRNAs. In addition, the number of exons was lower in lncRNAs than in mRNAs and their exons were longer. TCDD affected the expression of 22 lncRNAs (differentially expressed lncRNAs [DELs]; log2 fold change ≥ 1, P-adjusted < 0.05) in the examined cells. Potential functions of DELs were indirectly predicted via searching their target cis- and trans-regulated protein-coding genes. The co-expression analysis revealed that DELs may influence the expression of numerous genes, including those involved in cellular response to xenobiotics, dioxin metabolism, endoplasmic reticulum stress and cell proliferation. Aryl hydrocarbon receptor (AhR) and cytochrome P450 1A1 (CYP1A1) were found among the trans-regulated genes.ConclusionsThese findings indicate that the identified lncRNAs may constitute a part of the regulatory mechanism of TCDD action in granulosa cells. To our knowledge, this is the first study describing lncRNAs in porcine granulosa cells as well as TCDD effects on the lncRNA expression profile. These results may trigger new research directions leading to better understanding of molecular processes induced by xenobiotics in the ovary.
Highlights
Long non-coding RNAs may regulate gene expression in numerous biological processes including cellular response to xenobiotics
It was found that Long non-coding RNAs (lncRNAs) regulate gene expression via numerous mechanisms. lncRNAs may be implicated in e.g., chromatin organization, epigenetic modification, transcriptional regulation, RNA processing and modification, regulation of miRNA activity as well as protein stability or cellular protein localization [3, 8, 9]. lncRNAs seem to be involved in many fundamental biological processes including maintenance and induction of stem cell pluripotency, cell differentiation, cell proliferation and apoptosis [6, 8]
The stringency of the selection process was increased by discarding transcripts which blasted to small RNAs annotated in the Rfam database
Summary
Long non-coding RNAs (lncRNAs) may regulate gene expression in numerous biological processes including cellular response to xenobiotics. Recent advances in RNA sequencing (RNA-Seq) technologies led to the discovery of tens of thousands non-coding RNAs (ncRNAs) across the entire transcriptomes of many species. It was demonstrated that lncRNA sequences are not highly conserved and their expression profiles differ among species, developmental stages and cell types. Due to their variable nature, lncRNAs are still poorly characterized [7, 8]. The results of recent studies indicate that lncRNAs take an active part in cellular response to various xenobiotics [1]
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