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. 2022 Dec 16;12(24):3561.
doi: 10.3390/ani12243561.

Differential Expression Analysis of tRNA-Derived Small RNAs from Subcutaneous Adipose Tissue of Obese and Lean Pigs

Hao Gu  1   2 , Mailin Gan  1   2 , Linghui Wang  1   2 , Yiting Yang  1   2 , Jinyong Wang  3 , Lei Chen  1   2 , Shunhua Zhang  1   2 , Ye Zhao  1   2 , Lili Niu  1   2 , Dongmei Jiang  1   2 , Yiwu Chen  4 , Anan Jiang  1   2 , Linyuan Shen  1   2 , Li Zhu  1   2
Affiliations

Differential Expression Analysis of tRNA-Derived Small RNAs from Subcutaneous Adipose Tissue of Obese and Lean Pigs

Hao Gu et al. Animals (Basel). .

Abstract

Epigenetic factors, including non-coding RNA regulation, play a vital role in the development of obesity and have been well researched. Transfer RNA-derived small RNA (tsRNA) is a class of non-coding RNA proven to be involved in various aspects of mammalian biology. Here we take pigs as a model for obesity research and use tsRNA-seq to investigate the difference in tsRNA expression in the subcutaneous adipose tissue of obese and lean pigs to elucidate the role of tsRNA in obesity development. A total of 482 tsRNAs were identified in pig adipose tissue, of which 123 were significantly differentially accumulated tsRNAs compared with the control group. The tRF-5c was the main type of these tsRNAs. The largest number of tsRNAs produced was the Gly-carrying tRNA, which produced 81 tsRNAs. Functional enrichment analysis revealed that differential tsRNAs indirectly participated in MAPK, AMPK, insulin resistance, the TNF signaling pathway, adipocytokine signaling pathway, and other signaling pathways by interacting with target genes. These are involved in bioenergetic metabolic regulatory processes, suggesting that tsRNAs may influence these pathways to mediate the regulation of energy metabolism in porcine adipocytes to promote lipid deposition, thus contributing to obesity. Our findings suggest a potential function of tsRNA in regulating obesity development.

Keywords: lipid deposition; obese; pig; subcutaneous adipose tissue; tsRNA.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phenotypic indexes of obese and lean pigs. (A) The percentage of adipose tissue in the carcass. (B) Subcutaneous fat thickness in different parts of the carcass. (C) Subcutaneous adipose tissue by HE staining. (D) Adipocyte volume; HDL (E), LDL (F), vLDL (G), TG (H), and TC (I) in the serum of obese and lean pigs. * p < 0.05, ** p < 0.01, *** p < 0.001.
Figure 2
Figure 2
Characteristics of tsRNA in the subcutaneous adipose tissue of lean and obese pigs. (A) The number of tsRNAs derived from different tRNA isoforms. (B) Types of tsRNAs produced by tRNAs carrying different amino acids. (C) Different tsRNA types specific to obese and lean subcutaneous fat. (D) Venn diagram of tsRNA quantity in obese and lean subcutaneous fat. (E) Percentage of different types of tsRNA. (F) tsRNA length distribution.
Figure 3
Figure 3
Analysis of differentially expressed tsRNAs. Scatter plot (A) and a volcano plot (B) of differentially expressed tsRNA, red dots represent increased tsRNA in obese pigs compared with lean pigs, blue dots represent decreased tsRNA in obese pigs compared with lean pigs. (C) RT-qPCR verified tsRNA sequencing results (n = 6). (D,E) Bias of differentially expressed tsRNA seed sequences.
Figure 4
Figure 4
tsRNA target genes prediction and GO enrichment analysis. (A) The number of target genes and gene intersection distribution; GO enrichment analysis of target genes of increased (B), significantly increased (C), and significantly decreased (D) tsRNAs.
Figure 5
Figure 5
KEGG enrichment analysis of tsRNA target genes. Increased (A), significantly increased (B), and significantly decreased (C) tsRNA target gene KEGG signaling pathway enrichment analysis.
Figure 6
Figure 6
tsRNA-target gene-pathways network interactions. Diagram of the regulation network of tsRNA-target gene-fat development-related pathways. The red line indicates differential upregulation of tsRNA, the blue line indicates differential downregulation.
Figure 7
Figure 7
tsRNA regulatory network and correlation analysis. (A–D) Detection of relevant gene expression levels by RT-qPCR (n = 6). (E) Heat map of correlation between tsRNA and selected genes in metabolic pathways. * p < 0.05, ** p < 0.01.
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