Supplementary Material.zip

Age-related thymic involution is one of the causes of induced immunity decline. Recent evidences indicated that long noncoding RNAs (lncRNAs) are widely involved in regulating organ development. In this experiment, thymus weight gradually decreased after 1-month-old and adipocytes gradually deposited with age. Besides, RNA sequencing showed that 265 differentially expressed lncRNAs (DELs) and 340 differentially expressed genes (DEGs) were identified during development stage (1-month-old) and involution stages (3-month-old and 6-month-old) in males, and 131 DELs and 154 DEGs in females. Functional analysis showed that DEGs were mainly enriched in cell adhesion, potassium ion transport, activation of immune response, inflammatory response and humoral immune response. Next, based on the STRING database, 16 DEGs were identified to be co-expressed in the male and female protein-protein interaction (PPI) networks. Meanwhile, 15 causal transcription factors were identified via analyzing the promoter sequence of male and female DEGs. To further analyze the regulatory mechanism of key DEGs, miRWalk 3.0 was used to predict the targeting relationship between DEGs and miRNAs. Then, the targeting relationship between DELs co-expressed in males and females and related miRNAs were predicted via TargetScan and miranda. Finally, we successfully constructed a novel lncRNA–miRNA–mRNA network with Cytoscape. Quantitative real-time PCR results showed that RNAs related to adipocyte deposition in the lncRNA-miRNA-mRNA network were mainly highly expressed in thymic epithelial cells. In summary, this experiment systematically identified and analyzed the expression profiles of lncRNAs and genes during the early stages of thymic involution for the first time, which provided valuable reference for further exploring the roles of lncRNAs in thymic involution.