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Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes. We performed <i>de novo</i> transcriptome assembly to characterize lncRNAs in spermatozoa, and to investigate the role of the potential target genes of the differentially expressed lncRNAs (DElncRNAs) in sperm freezability. We detected approximately 4007 DElncRNAs, which were differentially expressed in spermatozoa from boars classified as having good and poor semen freezability (GSF and PSF, respectively). Most of the DElncRNAs were upregulated in boars of the PSF group and appeared to significantly affect the sperm’s response to the cryopreservation conditions. Furthermore, we predicted that the potential target genes were regulated by DElncRNAs in <i>cis</i> or <i>trans</i>. It was found that DElncRNAs of both freezability groups had potential <i>cis</i>- and <i>trans</i>-regulatory effects on different protein-coding genes, such as <i>COX7A2L</i>, <i>TXNDC8</i> and <i>SOX-7</i>. Gene Ontology (GO) enrichment revealed that the DElncRNA target genes are associated with numerous biological processes, including signal transduction, response to stress, cell death (apoptosis), motility and embryo development. Significant differences in the <i>de novo</i> assembled transcriptome expression profiles of the DElncRNAs between the freezability groups were confirmed by quantitative real-time PCR analysis. This study reveals the potential effects of protein-coding genes of DElncRNAs on sperm functions, which could contribute to further research on their relevance in semen freezability.