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Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition

ABSTRACT: The identification of the molecular mechanisms regulating pathways associated to the potential of fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of fat traits. MicroRNAs (miRNAs) interactions with target RNAs regulate gene expression and modulate pathway activation in cells and tissues. In pigs, miRNA discovery is well far from saturation and the knowledge of miRNA expression in backfat tissue and particularly of the impact of miRNA variations are still fragmentary. We characterized by RNA-seq the small RNAs (sRNAs) expression profiles in Italian Large White pig backfat tissue. Comparing two groups of pigs divergent for backfat deposition, we detected 31 significant differentially expressed (DE) sRNAs, 14 up-regulated (including ssc-miR-132 ,ssc-miR-146b, ssc-miR-221-5p, ssc-miR-365-5p, and the moRNA ssc-moR-21-5p) and 17 down-regulated (including ssc-miR-136, ssc-miR-195, ssc-miR-199a-5p, and ssc-miR-335). To understand the biological impact of the observed miRNA expression variations, we used the expression correlation of DE miRNA target transcripts expressed in the same samples to define a regulatory network of 193 interactions between DE miRNAs and 40 DE target transcripts showing opposite expression profiles and being involved in specific pathways. Several miRNAs and mRNAs in the network resulted to be expressed from backfat related pig QTLs. These results are informative on the complex mechanisms influencing fat traits, shed light on a new aspect of the genetic regulation of fat deposition in pigs, and facilitate the perspective implementation of innovative strategies of pig genetic improvement based on genomic markers.

ORGANISM(S): Sus scrofa

PROVIDER: GSE108829 | GEO | 2018/08/31

REPOSITORIES: GEO

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Project description:Sertoli cells (SCs), the only somatic constituent of the testicular seminiferous epithelium, are vital to spermatogenesis. We previously found that vitamin C (ascorbic acid, AA) can reprogram the transcriptome, and promote the proliferation and reproductive function of pig immature SCs (iSCs). However, the global change of microRNAs (miRNA) expression and its effect on pig iSCs as induced by vitamin C treatment is still unknown. Here, we performed small RNA sequencing on pig iSCs after 250μM AA2P (L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate) treatment for 36h. Total number of detected miRNAs ranged from 326-335 known, and 400-570 novel miRNAs. Of the top ten highly expressed miRNAs, we found that 8 were common (miR-21-5p, let-7i-5p, miR-30a-5p, let-7f-5p, let-7g, miR-100, miR-10a-5p and miR-30d), which were predicted to target mRNAs involved in cell development and differentiation. We identified 78 differentially expressed (DE) miRNAs (|log2 foldchange|≥1; Padj.<0.05), including 7 known and 71 novel miRNAs. We further selected 13 highly and stably expressed DE miRNAs (4 up-regulated: miR-184, novel-miR-610, novel-miR-316 and novel-miR-1274; 9 down-regulated: miR-222, miR-221-5p, miR-221-3p, miR-210, miR-146b, miR-146a-5p, novel-miR-182, novel-miR-1088 and novel-miR-1016), and performed integrated analysis on the miRNA-mRNA regulatory network. DE mRNAs negatively targeted by these 13 DE miRNAs were enriched in multiple GO and KEGG signaling pathways (e.g. pyruvate and steroid metabolic processes, developmental process in reproduction, response to oxidative stress, Glycolysis/Gluconeogenesis and HIF-1). We validated 8 DE miRNAs and their 12 DE mRNA targets, with expression patterns consistent with (mi)RNA-seq results. Taken together, our findings demonstrate that vitamin C could induce the global change of miRNAs, which possibly regulate cell proliferation, energy metabolism and male reproduction as induced by vitamin C treatment on pig iSCs.

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Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition

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