Genome-Wide Identification and Functional Analysis of Long Noncoding RNAs in Swine Ovarian Follicles during the Onset of Puberty

Long noncoding RNAs (lncRNAs) have been recently considered to regulate animal development, yet their function in swine ovarianfollicles during the onset of puberty remains almost unexplored. To identify the genes that regulate the onset of puberty in swine,we measured the expression levels of lncRNAs and mRNAs from large follicles in the ovaries of swine. We conducted RNA sequencinganalysis to examine the largest follicles (diameter range from 3 to = 5 mm) on ovaries of pre-pubertal gilts (case; n=3), and those(diameter = 5 mm) on ovaries of in-pubertal (control; n=3) gilts. Results yielded 18891 predicted lncRNAs, including 123 differentiallyexpressed lncRNAs, corresponding to 298 target genes. We also studied the role of cis- and trans-acting lncRNAs that regulate theexpression of target genes and found several lncRNAs involved in the regulation of puberty and reproduction, as well as severalpathways related to these processes. For instance, the oxytocin signaling pathway and ECM receptor interaction weresignificantly enriched (adj P < 0.05) as demonstrated by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Our resultsindicate that lncRNAs play a vital role in regulating puberty in swine. However, further research is needed to explore thefunctions of lncRNAs and their predicted targets to provide a detailed expression profile of lncRNAs associated with puberty inswine.

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