RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats

SIMPLE SUMMARY: Long intergenic non-coding RNAs (lincRNAs) can regulate testicular development by acting on protein-coding genes. Therefore, it is important to explore the expression patterns and roles of lincRNAs during the postnatal development of the goat testis. In this study, the testes of Yiling goats with average ages of 0, 30, 60, 90, 120, 150, and 180 days postnatal were used for RNA-seq. In total, 20,269 lincRNAs were identified, including 16,931 novel lincRNAs. Using weighted gene co-expression network analysis, seven time-specifically diverse lincRNA modules and six mRNA modules were identified. Dramatically, the down-regulation of growth-related lincRNAs was nearly one month earlier than the up-regulation of spermatogenesis-related lincRNAs, while the down-regulation of growth-related protein-coding genes and the correspondent up-regulation of spermatogenesis-related protein-coding genes occurred at the same age. Moreover, potential lincRNA target genes were predicted. Moreover, key lincRNAs in the process of testis development were predicted, such as ENSCHIT00000000777, ENSCHIT00000002069, and ENSCHIT00000005076. In the present study, the divergent regulation patterns of lincRNA on spermatogenesis and testis growth were discovered. This study can improve our understanding of the functions of lincRNAs in the regulation of testis development. ABSTRACT: Long intergenic non-coding RNAs (lincRNAs) regulate testicular development by acting on protein-coding genes. However, little is known about whether lincRNAs and protein-coding genes exhibit the same expression pattern in the same phase of postnatal testicular development in goats. Therefore, this study aimed to demonstrate the expression patterns and roles of lincRNAs during the postnatal development of the goat testis. Herein, the testes of Yiling goats with average ages of 0, 30, 60, 90, 120, 150, and 180 days postnatal (DP) were used for RNA-seq. In total, 20,269 lincRNAs were identified, including 16,931 novel lincRNAs. We identified seven time-specifically diverse lincRNA modules and six mRNA modules by weighted gene co-expression network analysis (WGCNA). Interestingly, the down-regulation of growth-related lincRNAs was nearly one month earlier than the up-regulation of spermatogenesis-related lincRNAs, while the down-regulation of growth-related protein-coding genes and the correspondent up-regulation of spermatogenesis-related protein-coding genes occurred at the same age. Then, potential lincRNA target genes were predicted. Moreover, the co-expression network of lincRNAs demonstrated that ENSCHIT00000000777, ENSCHIT00000002069, and ENSCHIT00000005076 were the key lincRNAs in the process of testis development. Our study discovered the divergent regulation patterns of lincRNA on spermatogenesis and testis growth, providing a fresh insight into age-biased changes in lincRNA expression in the goat testis.