Dynamic Transcriptome Analysis Reveals Potential Long Non-coding RNAs Governing Postnatal Pineal Development in Pig

Postnatal development and maturation of pineal gland is a highly dynamic period of tissue remodeling and phenotype maintenance, which is genetically controlled by programmed gene expression regulations. However, limited molecular characterization, particularly regarding long noncoding RNAs (lncRNA), is available for postnatal pineal at a whole transcriptome level. The present study first characterized the comprehensive pineal transcriptome profiles using strand-specific RNA-seq to illustrate the dynamic mRNA/lncRNA expression at three developmental stages (infancy, puberty, and adulthood). The results showed that 21,448 mRNAs and 8,166 novel lncRNAs were expressed in pig postnatal pineal gland. Among these genes, 3,573 mRNAs and 851 lncRNAs, including the 5-hydroxytryptamine receptors, exhibited significant dynamic regulation along maturation process, while the expression of homeobox genes didn’t show significant differences. Gene Ontology analysis revealed that the differentially expressed genes (DEGs) were significantly enriched in ion transport and synaptic transmission, highlighting the critical role of calcium signaling in postnatal pineal development. Additionally, co-expression analysis revealed the DEGs could be grouped into 12 clusters with distinct expression patterns. Many differential lncRNAs were functionally enriched in co-expressed clusters of genes related to ion transport, transcription regulation, DNA binding, and visual perception. Our study first provided an overview of postnatal pineal transcriptome dynamics in pig and demonstrated that dynamic lncRNA regulation of developmental transitions impact pineal physiology.