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

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.

Identification of potential tissue-specific biomarkers involved in pig fat deposition through integrated bioinformatics analysis and machine learning

“…Fifty-six DEGs were filtered out, with 27 down- and 29 up-regulated genes in the BT group. Functional analysis of these DEGs indicated that these targets were primarily associated with the synthesis and metabolism of fats and fatty acids, the energy balance of the organism, such as the carboxylic acid metabolic/biosynthetic process [ 31 ], PPAR signaling pathway [ 32 ], ECM-receptor interaction [ 33 ] and AMPK signaling pathway [ 34 ]. These pathways aberrant expression genes mainly contained FASN , ME1 and ACLY among the DEGs.…”

Identification of tRNA-derived RNAs in adipose tissue from overweight type 2 diabetes mellitus patients and their potential biological functions

“…These two tsRNAs belong to the same tRF-5c family. A study by Gu et al in which tsRNAs were sequenced in subcutaneous fat from fat and lean pigs found that tsRNAs were not produced by random cleavage of tRNAs, that tRF-5c was the predominant type of tsRNA in differential lipid deposition, and that tRF-5c may be inextricably linked to lipid metabolism (33). The tRF-1-28-Glu-TTC-3-M2 was found to be associated with circadian rhythm and AMPK signaling by KEGG enrichment analysis.…”

tsRNA Landscape and Potential Function Network in Subcutaneous and Visceral Pig Adipose Tissue

“…The tsRNA sequencing dataset was obtained from a previous study [ 32 ]. The miRNA data used the same library as tsRNAs, and Bowtie software was used to map clean reads to miRNAs sequences in miRBase ( , accessed on 18 November 2022).…”