Circular RNA Profiling Identifies Novel circPPARA that Promotes Intramuscular Fat Deposition in Pigs

Abstract

Intramuscular fat (IMF) content plays an important role in pork quality. Circular RNAs (circRNAs) implicate various biological processes; however, the regulatory mechanisms and functions of circRNAs in porcine IMF remains elusive. Hence, the study assessed the circRNA expression profiling in the longissimus dorsi muscle of pigs with high (H) and low (L) IMF content to unravel their regulatory functions in improving meat quality. The RNA sequencing analysis identified 29,732 circRNAs from six sampled pigs, most of which were exon-derived. In the muscle, 336 were differentially expressed (DE) between the H and L IMF groups; 196 circRNAs were upregulated, and 140 were downregulated. Subsequent qRT-PCR validation of 10 DE circRNAs revealed expression patterns consistent with the RNA-seq data. Gene ontology and KEGG enrichment analysis revealed that most significantly enriched DE circRNAs’ host genes were linked to lipid metabolism and adipogenesis processes. The circRNA–miRNA regulatory network analysis found several circRNAs targeting miRNAs associated with adipogenesis. Finally, a novel circRNA, circPPARA, was identified with the expression positively correlated with the IMF content. Detailed analysis revealed that circPPARA was formed via head-to-tail splicing and was more stable than the linear PPARA, predominantly located in the cytoplasm. Functional studies using overexpression and siRNA constructs demonstrated that circPPARA promotes differentiation and hinders the proliferation of porcine intramuscular preadipocytes. Moreover, the dual-luciferase assay revealed that circPPARA adsorbed miR-429 and miR-200b, thereby promoting intramuscular adipogenesis in pigs. Our results identified a candidate circRNA, circPPARA, that affects porcine IMF content. The study provides knowledge of the regulatory functions of circRNAs in intramuscular adipogenesis and abundant resource for future research on circRNAs in pigs.

Characterization of circular RNA profiles of oviduct reveal the potential mechanism in prolificacy trait of goat in the estrus cycle

“…Further analysis showed that the circRNAs identified were mainly generated by cyclization of gene exons ( Zhang M. L. et al, 2018 ), in the sheep ( Lv et al, 2020 ) and cattle ( Liu et al, 2020 ), indicating similar origins of circRNAs in different species. In our present study, we found that the majority of circRNAs are less than 10,000 nt in length, which is consistent with the results of a previous study in goat ovary ( Liu et al, 2022 ), but longer than circRNAs identified in goat endometrial ( Li et al, 2022 ), indicating that the longer the sequence, the greater the corresponding increase in the difficulty of circRNA loop formation. Moreover, most of the identified circRNAs were typically distributed on chromosomes 1-11, and the expression of circRNAs in the luteal phase was more abundant than that in the follicular phase of the oviduct, indicating that the functions of circRNAs in the oviduct are diverse.…”

Comprehensive Analysis of Circular RNAs in Porcine Small Intestine Epithelial Cells Associated with Susceptibility to Escherichia coli F4ac Diarrhea

“…The calculation formula was as follows: SRPBM = (Back spliced junction reads / Total number of mapped reads)×10 9 .…”

Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes

“…As a polygenic trait, IMF is a complex metabolic process determined by the hyperplasia and hypertrophy of adipocytes and involves many biological processes and pathways, which are regulated by various molecules, such as hormones, transcription factors, protein-coding genes, and non-coding RNAs [ 10 , 11 , 12 ]. However, when compared with other traits, dissecting the genetic basis of IMF content is still limited, owing to its complexity.…”

“…Further, LMFlnc1 (lncRNA) promotes adipogenesis in porcine IMF cells by upregulating CAV-1 expression via miR-199a-5p [ 14 ]. Moreover, Sus_circPPARA promotes differentiation and hinders proliferation in porcine intramuscular preadipocytes [ 11 ]. Despite the increasing number of transcriptomic studies aimed at dissecting IMF deposition, cascade events related to this trait remain mostly unknown.…”

“…However, commercial pig breeds, such as Duroc, Landrace, and Yorkshire, are selected for better lean muscle growth, leading to a decrease in the deposition of fat, including IMF, resulting in reduced meat palatability [ 12 ]. Studies have also shown that IMF varies considerably among pure commercial breeds [ 7 , 11 , 16 ]. For example, Yorkshire pigs are a typical lean-type Western breed and have a low level of fat deposition as a whole.…”