Systematic analysis of the regulatory functions of microRNAs in chicken hepatic lipid metabolism

Abstract

Laying performance is an important economic trait in hens, and this physiological process is largely influenced by the liver function. The livers of hens at 20- and 30-week-old stages were investigated using the next generation sequencing to identify the differences of microRNA expression profiles. Compared with the 20-week-old hens, 67 down- and 13 up-regulated microRNAs were verified to be significant differentially expressed (false discovery rate, FDR ≤ 0.05) (SDE) in the 30-week-old. We also identified 13 down- and 6 up-regulated novel differentially expressed (DE) microRNAs. miR-22-3p and miR-146b-5p, which exhibit critical roles in mammalian lipid metabolism, showed the most abundant expression and the highest fold-change, respectively. A total of 648 potential target genes of the SDE microRNAs were identified through an integrated analysis of microRNAs and the DE genes obtained in previous RNA-sequencing, including FADS1, FADS2, ELOVL6 and ACSL5, which are critical lipid metabolism-related regulators. Bioinformatic analyses revealed that target genes were mainly enriched in lipid-related metabolism processes. This work provides the first study of the expression patterns of hepatic microRNAs between 20- and 30-week old hens. The findings may serve as a fundamental resource for understanding the detailed functions of microRNAs in the molecular regulatory systems of lipid metabolism.

Figure 1. Distribution of different sRNA classes in the miRNA-seq data.

L20, library prepared from the livers of 20-week-old chickens; L30, library prepared from the livers of 30-week-old chickens.

Figure 2. Length distribution of miRNA sequences from the livers of 20- and 30-week-old chickens.

Figure 3. Top ten most abundantly expressed miRNAs in the livers of 20- and 30-week-old chickens.

**FDR ≤ 0.05.

Figure 4. QRT-PCR verification of differentially expressed miRNAs.

*P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001. Fold-change > 0 indicates up-regulation; fold-change < 0 indicates down-regulation.

Figure 5. The putative target genes of miR-22-3p.

Figure 6. Enriched GO terms of differentially expressed genes targeted by the significant differentially expressed miRNAs.

Only the significantly enriched (P ≤ 0.05) GO terms in the biological process, cellular component, and molecular function categories are presented.

Figure 7. Integrated analysis of miRNAs and their target genes enriched in significant pathways.

Circle indicates miRNA, and square indicates target gene. Green indicates down-regulation, and red indicates up-regulation. The letter in the bracket after the target gene indicates the abbreviation of the related pathways as follows: Pa-Pantothenate and CoA biosynthesis, B-Biosynthesis of unsaturated fatty acids, G-Glycerophospholipid metabolism, PP-PPAR signalling pathway, and S-Steroid biosynthesis.