Integrated transcriptomic characterization and ceRNA network analysis during early liver development in goat kids

The transition from milk to solid feed after birth drives the metabolic reprogramming of the liver in mammals, yet the underlying transcriptional regulatory mechanisms remain poorly understood. In this study, we characterized the dynamic transcriptomic profiles of liver tissues in goat kids from birth to post-weaning (1 d, 2 wk, 4 wk, 8 wk, and 12 wk of age) to elucidate the competing endogenous RNA (ceRNA) regulatory network underlying metabolic adaptation. Weighted gene co-expression network analysis revealed that differentially expressed genes, including PPARG, FASN, FABP3, SCD, ELOVL5, and ELOVL6, were significantly enriched in the PPAR signaling pathway and fatty acid biosynthesis pathway and exhibited high expression during the suckling period. This expression pattern suggests active hepatic lipogenesis supporting rapid growth in suckling kids, while the reliance on endogenous lipid synthesis decreased after weaning. Additionally, we identified 567 differentially expressed long non-coding RNAs (DELs). Among these, target genes of DELs in Cluster 12 and Cluster 14 were significantly enriched in immune-related pathways, such as NF-κB and Th17 cell differentiation. Their dynamic expression patterns suggest potential roles in mediating the transition from passive to active immunity and in responding to weaning stress. Furthermore, a lipid metabolism-associated ceRNA network was constructed, including miR-154b-3p/miR-197-3p-ACACB-MSTRG.10418.2 and miR-497-5p-FASN-MSTRG.9465.3 axes. The targeting relationship within the miR-497-5p-FASN-MSTRG.9465.3 axis was experimentally validated. These findings provide novel insights into the regulatory mechanisms underlying early liver development and metabolic adaptation in ruminants.