The landscape of the long non-coding RNAs and circular RNAs of the abdominal fat tissues in the chicken lines divergently selected for fatness

Abstract

Background Excessive deposition of abdominal fat poses serious problems in broilers owing to rapid growth. Recently, the evolution of the existing knowledge on long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have established their indispensable roles in multiple physiological metabolic processes, including adipogenesis and fat deposition. However, not much has been explored on their profiles in the abdominal fat tissues of broilers to date. In the study, we aimed to characterize the vital candidates of lncRNAs and circRNAs and their underlying regulations for abdominal fat deposition in broilers. Results The present study sequenced the lncRNAs and circRNAs expression profiles in the abdominal fat tissues isolated from 7-week-old broilers, who were divergently selected for their fatness. It identified a total of 3359 lncRNAs and 176 circRNAs, demonstrating differential expressed (DE) 30 lncRNAs and 17 circRNAs between the fat- and lean-line broilers (|log2FC| ≥ 1, P < 0.05). Subsequently, the 20 cis-targets and 48 trans-targets of the candidate DE lncRNAs were identified for depositing abdominal fat by adjacent gene analysis and co-expression analysis, respectively. In addition, the functional enrichment analysis showed the DE lncRNAs targets and DE circRNAs host genes to be mainly involved in the cellular processes, amino/fatty acid metabolism, and immune inflammation-related pathways and GO terms. Finally, the vital 16 DE lncRNAs located in cytoplasm and specifically expressed in fat/lean line and their targets were used to construct the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) regulatory network, comprising 7 DE lncRNAs, 28 miRNAs, 11 DE mRNAs. Notably, three lncRNAs including XR_001468036.2, XR_003077610.1 and XR_001466431.2 with the most connected degrees might play hub regulatory roles in abdominal fat deposition of broilers. Conclusions This study characterized the whole expression difference of lncRNAs and circRNAs between the two lines broilers with divergently ability of abdominal fat. The vital candidate DE lncRNAs/circRNAs and ceRNA regulations were identified related to the deposition of abdominal fat in chicken. These results might further improve our understanding of regulating the non-coding RNAs in obesity.

Strand-Specific RNA Sequencing Reveals Gene Expression Patterns in F1 Chick Breast Muscle and Liver after Hatching

“…In addition, the TGFB2 T (−640) > C SNP was associated with growth and body composition traits in a broiler chicken [46]. As a member of the fibroblast growth factor (FGF) gene family, FGF1 plays a role in adipocyte differentiation and adipose tissue remodeling [47]. In chickens, FGF1 gene expression is positively correlated with intramuscular fat content in male thigh muscle but showed a negative correlation in female birds [48].…”

miR-128-3p inhibits intramuscular adipocytes differentiation in chickens by downregulating FDPS

“…MicroRNAs (miRNAs) are short noncoding RNAs of approximately 22 nucleotides that negatively regulate gene expression at the posttranscriptional level by recognizing the 3′ UTR of a target mRNA [ 12 – 14 ]. Studies have shown that miRNAs are involved in regulating various biological processes, including lipid metabolism, adipogenesis, cell proliferation and cell differentiation [ 15 – 17 ]. For instance, miR-33a inhibits the differentiation of bovine preadipocytes through the IRS2-Akt pathway [ 18 ].…”