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Long non-coding RNAs and mRNAs profiling of liver tissue during four developmental stages in chickens

ABSTRACT: Liver is the major organ of lipid biosynthesis in chicken. In laying hens, the liver synthesizes most of yolk precursors and transports to the developing follicles to produce eggs. However, a systematic and comprehensive investigation of long non-coding RNAs (lncRNAs) and mRNAs transcriptome in chicken liver across different developmental stages remain clearly unknown. Here, we constructed 12 RNA libraries from liver tissue during four developmental stages, including juvenile period (JP, day 60), sexual maturity period (SM, day 133), peak laying period (PL, day 220) and broodiness period (BP, day 400). A total of 16,930 putative lncRNAs and 18,260 mRNAs were identified among these samples. More than half of identified lncRNAs were intergenic lncRNAs (lincRNAs), accounting for 53.70%. The temporal expression pattern showed that lncRNAs were more restricted than mRNAs. We identified numerous differentially expressed lncRNAs (DE lncRNA) and mRNAs (DEGs) by pairwise comparisons between the four developmental stages and found that vitellogenin 2 (VTG2), riboflavin binding protein (RBP), and a novel protein-coding gene were differentially expressed in all stages. Time-series analysis showed that the module with up-regulated genes were enriched in related to lipid metabolism process. Co-expression networks suggested the functional relatedness between mRNAs and lncRNAs and the results showed the DE-lncRNAs also mainly involve in lipid biosynthesis and metabolism process. These results suggest the transcriptome variation of liver in different developmental stages and improve the comparative understandings of molecular mechanisms of liver development in chickens.

ORGANISM(S): Gallus gallus

PROVIDER: GSE138152 | GEO | 2020/06/05

REPOSITORIES: GEO

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Project description:In this study, RNA-Seq technology was adopted to investigate the differences in expression profiles of the hepatic lipid metabolism-related genes and the associated pathways between juvenile and laying hens. RNA-Seq analysis was carried out to estimate total RNA harvested from the liver of juvenile hens (n = 3) and laying hens (n = 3). Compared with juvenile hens, 2574 differentially expressed (DE) genes (1487 down and 1087 up) with P â¤ 0.05 were obtained, and 955 of these genes were significantly DE (SDE) at a false discovery rate (FDR) of 0.05 and fold-change â¥ 2 in laying hens. There were 198 SDE novel genes (107 down-regulated and 91 up-regulated) (FDR â¤ 0.05) that were obtained from the transcriptome, and most of them were highly expressed. Moreover, 332 SDE isoforms were identified. Gene Ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that SDE genes were significantly associated with steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P â¤ 0.05). The top significantly enriched GO terms included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction suggesting the principal lipogenesis in the liver of laying hens. This study suggests that the major changes at the level of transcriptome in laying hen liver are closely related to fat metabolism. Some highly differentially expressed uncharacterized novel genes and alternative splicing isoforms detected might also take part in lipid metabolism, though it needs investigation. Therefore, this study provides valuable information of mRNA of chicken liver, and deeper functional investigations on the mRNAs could help explore or provide new insights into molecular networks of lipid metabolism in chicken liver. The liver expression profile of juvenile hens and laying hens were generated by RNA-seq.

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Long non-coding RNAs and mRNAs profiling of liver tissue during four developmental stages in chickens

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