Table_3_Dynamic Transcriptome Analysis Reveals Potential Long Non-coding RNAs Governing Postnatal Pineal Development in Pig.XLSX

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.

松果体（pineal gland）的出生后发育与成熟是组织重塑与表型维持的高度动态过程，该过程受程序化基因表达调控的遗传控制。然而，目前在全转录组层面上对出生后松果体的分子特征研究较为有限，针对长链非编码RNA（long noncoding RNAs，lncRNA）的相关研究更是不足。本研究首次采用链特异性RNA测序（strand-specific RNA-seq）技术对松果体的全面转录组特征进行解析，以阐明猪在幼年期、青春期及成年期三个发育阶段的mRNA/lncRNA动态表达模式。结果显示，在猪出生后松果体中共检测到21448条mRNA以及8166条新型lncRNA。在这些基因中，共有3573条mRNA和851条lncRNA（包括5-羟色胺受体）随成熟过程呈现显著的动态表达调控，而同源盒基因（homeobox genes）的表达则未出现显著差异。基因本体（Gene Ontology，GO）富集分析显示，差异表达基因（differentially expressed genes，DEGs）显著富集于离子转运与突触传递通路，凸显了钙信号通路在出生后松果体发育中的关键作用。此外，共表达分析显示差异表达基因可被划分为12个具有独特表达模式的基因簇。大量差异lncRNA在与离子转运、转录调控、DNA结合及视觉感知相关的基因共表达簇中实现功能富集。本研究首次对猪出生后松果体的转录组动态变化进行了系统性概述，并证实发育进程中的动态lncRNA调控可影响松果体生理功能。