3’UTR-Seq analysis of chicken abdominal adipose tissue reveals widespread intron retention in 3’UTR and provides insight into molecular basis of feed efficiency

Abstract

Feed efficiency (FE) is an important trait in the broiler industry due to its direct correlation to efficient muscle growth instead of fat deposition. The present study characterized and compared gene expression profiles in abdominal fat from broiler chickens of different FE levels to enhance the understanding of FE biology. Specifically, traditional whole-transcript RNA-sequencing (RNA-seq) and 3’ UTR-sequencing (3’ UTR-seq) were applied to 22 and 61 samples, respectively. Overall, these two sequencing techniques shared a high correlation (0.76) between normalized counts, although 3’ UTR-seq showed a higher variance in sequencing and mapping performance statistics across samples and a lower rate of uniquely mapped reads. A higher percentage of 3’ UTR-seq reads mapped to introns suggested the frequent presence of cleavage sites in introns, thus warranting future research to study its regulatory function. Differential expression analysis identified 1198 differentially expressed genes (DEGs) between high FE (HFE) and intermediate FE (IFE) chickens with False Discovery Rate < 0.05 and fold change > 1.2. The processes that were significantly enriched by the DEGs included extracellular matrix remodeling and mechanisms impacting gene expression at the transcriptional and translational levels. Gene ontology enrichment analysis suggested that the divergence in fat deposition and FE in broiler chickens could be associated with peroxisome and lipid metabolism possibly regulated by G0/G1 switch gene 2 (G0S2).

Spatial transcriptomics reveals alterations in perivascular macrophage lipid metabolism in the onset of Wooden Breast myopathy in broiler chickens

“…Expression of SCD and apolipoprotein 1 ( APOA1 ), indicators of elevated cholesterol efflux and biosynthesis of mono unsaturated FA 14 , coincided with the significantly elevated lipid level in WB 2 , 4 , 26 . Unlike in adipose tissue of high feed efficiency broilers (low-fat phenotype), G0/G1 switch gene 2 ( G0S2 ) was activated in the LLM, shifting towards a metabolism favoring lipid deposition 27 . Moreover, oxLDL- CD36 mediated signaling is associated with mitochondrial accumulation of long chain FA, possibly a consequence of enhanced FA oxidation and/or biosynthesis channeled by ACSL1 , and suppression of LLM migration which could explain the perivascular accumulation and cuffing by these cells 18 , 28 .…”

Spatial Transcriptomics Reveals Alterations in Perivascular Macrophage Lipid Metabolism: Insights into the onset of Wooden Breast Myopathy in Broiler Chickens

“…was activated in the LLM, shifting towards a metabolism favoring lipid deposition [25]. Moreover, oxLDL-CD36 mediated signaling is associated with mitochondrial accumulation of long chain FA, possibly a consequence of enhanced FA oxidation and/or biosynthesis channeled by ACSL1, and suppression of LLM migration which could explain the perivascular accumulation and cuffing by these cells [16,22].…”