Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China.
Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, 150030, People's Republic of China.
BMC Genomics. 2022 Dec 1;23(1):790. doi: 10.1186/s12864-022-09045-y.
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.
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.
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.
由于肉鸡生长迅速，腹部脂肪过度沉积会带来严重问题。最近，长链非编码 RNA（lncRNA）和环状 RNA（circRNA）的现有知识的发展已经确立了它们在包括脂肪生成和脂肪沉积在内的多种生理代谢过程中的不可或缺的作用。然而，迄今为止，关于它们在肉鸡腹部脂肪组织中的特征尚未得到充分探索。在本研究中，我们旨在鉴定 lncRNA 和 circRNA 的重要候选物及其在肉鸡腹部脂肪沉积中的潜在调控机制。
本研究对来自 7 周龄肉鸡的腹部脂肪组织进行了 lncRNA 和 circRNA 表达谱测序，这些肉鸡是根据其肥胖程度进行了差异选择。共鉴定出 3359 个 lncRNA 和 176 个 circRNA，其中脂肪型和瘦肉型肉鸡之间有 30 个 lncRNA 和 17 个 circRNA 表现出差异表达（|log2FC|≥1，P<0.05）。随后，通过邻近基因分析和共表达分析分别鉴定出候选差异表达（DE）lncRNA 的 20 个 cis 靶基因和 48 个 trans 靶基因，用于沉积腹部脂肪。此外，功能富集分析表明，DE lncRNA 靶基因和 DE circRNA 宿主基因主要参与细胞过程、氨基酸/脂肪酸代谢以及免疫炎症相关途径和 GO 术语。最后，鉴定出 16 个位于细胞质中且在脂肪/瘦肉系中特异性表达的重要 DE lncRNA 及其靶基因，构建了包含 7 个 DE lncRNA、28 个 miRNA、11 个 DE mRNA 的 lncRNA-miRNA-mRNA 竞争性内源 RNA（ceRNA）调控网络。值得注意的是，三个 lncRNA（包括 XR_001468036.2、XR_003077610.1 和 XR_001466431.2）的连接度最高，可能在肉鸡腹部脂肪沉积中发挥重要的调控作用。
本研究对具有不同腹部脂肪沉积能力的两系肉鸡的 lncRNA 和 circRNA 整体表达差异进行了描述。鉴定出与鸡腹部脂肪沉积相关的重要候选 DE lncRNA/circRNA 和 ceRNA 调控。这些结果可能进一步提高我们对肥胖相关非编码 RNA 调控的认识。
