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

ABSTRACT 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.