Full-length transcriptomic profiling of chicken liver metabolism under different feeding states using nanopore...

Feeding governs energy acquisition and drives state-specific hepatic metabolism. As the central metabolic and homeostatic organ in poultry, hepatic molecular mechanisms driving metabolic shifts pre- and post-feeding remain uncharacterized. We performed Oxford Nanopore full-length transcriptome sequencing on liver tissue from 6-week-old broilers under three energy states: ad libitum feeding (AL), fasting (F), and refeeding after fasting (RF). A total of 34,271 genes, 79,282 transcripts (including 6,605 annotated novel transcripts), 287 fusion transcripts, 74,892 simple sequence repeats, and 2,327 long non-coding RNAs (lncRNAs) were identified. Alternative polyadenylation (APA) analysis showed that AL and RF groups preferentially used proximal APA sites relative to the F group. Functional enrichment highlighted lipid and carbohydrate metabolism, autophagy, and mitophagy pathways. Differentially expressed transcripts (DETs) showed more differential events than differentially expressed genes (DEGs), and functional enrichment of DEGs, DETs, and differentially expressed lncRNAs in F vs AL and F vs RF comparisons mainly highlighted lipid, protein, carbohydrate, and xenobiotic metabolism pathways. Notably, enrichment analysis of APA, DEGs, and DETs between AL and RF identified the NOD-like receptor signaling pathway, a core innate immune signaling cascade, as one of the top altered pathways. Consistently, both F and RF groups displayed reduced expression of antimicrobial peptide genes (AvBD1, AvBD6, AvBD7, CATH2, CATH3) relative to the AL group, implying that short-term fasting may transiently suppress hepatic immune defense capacity. This study identifies numerous novel hepatic transcripts and demonstrates that, under distinct energy states, the liver maintains energy homeostasis via transcript-level expression shifts and APA site selection. These findings provide molecular insights into the metabolic responses and hepatic immune to fasting stress, laying a foundation for optimizing feeding regimens and improving liver health in broiler production.