Comprehensive analysis of differentially expressed circRNAs and ceRNA regulatory network in porcine skeletal muscle

Abstract

Background Circular RNA (circRNA), a novel class of non-coding RNA, has a closed-loop structure with important functions in skeletal muscle growth. The purpose of this study was to investigate the role of differentially expressed circRNAs (DEcircRNAs), as well as the DEcircRNA-miRNA-mRNA regulatory network, at different stages of porcine skeletal muscle development. Here, we present a panoramic view of circRNA expression in porcine skeletal muscle from Large White and Mashen pigs at 1, 90, and 180 days of age. Results We identified a total of 5819 circRNAs. DEcircRNA analysis at different stages showed 327 DEcircRNAs present in both breeds. DEcircRNA host genes were concentrated predominately in TGF-β, MAPK, FoxO, and other signaling pathways related to skeletal muscle growth and fat deposition. Further prediction showed that 128 DEcircRNAs could bind to 253 miRNAs, while miRNAs could target 945 mRNAs. The constructed ceRNA network plays a vital role in skeletal muscle growth and development, and fat deposition. Circ_0015885/miR-23b/SESN3 in the ceRNA network attracted our attention. miR-23b and SESN3 were found to participate in skeletal muscle growth regulation, also playing an important role in fat deposition. Using convergent and divergent primer amplification, RNase R digestion, and qRT-PCR, circ_0015885, an exonic circRNA derived from Homer Scaffold Protein 1 (HOMER1), was confirmed to be differentially expressed during skeletal muscle growth. In summary, circ_0015885 may further regulate SESN3 expression by interacting with miR-23b to function in skeletal muscle. Conclusions This study not only enriched the circRNA library in pigs, but also laid a solid foundation for the screening of key circRNAs during skeletal muscle growth and intramural fat deposition. In addition, circ_0015885/miR-23b/SESN3, a new network regulating skeletal muscle growth and fat deposition, was identified as important for increasing the growth rate of pigs and improving meat quality.

Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues

“…According to statistical data, we also found several significantly different host genes of circRNAs, including HOMER1 (host gene of novel_circ_0005314 and novel_circ_0005319), CDYL (host gene of novel_circ_0009256), INPP5F (host gene of novel_circ_0009845), LMO7 (host gene of novel_circ_0005934), and PPP2R3A (host gene of novel_circ_0000134), which might be involved in regulating the growth and development of muscle cells. Li et al analyzed the differential expression of the circRNA regulatory network in the skeletal muscles of Large White pigs and Mashen pigs at different ages and confirmed that circRNAs derived from Homer scaffold protein 1 (HOMER1) exons were differentially expressed during skeletal muscle growth, which might have certain significance for increasing the growth rate of pigs and improving meat quality ( 45 ). In a mouse knockout (KO) model, the excision of Homer1 resulted in obvious skeletal muscle myopathy, while in a study of rats, Jia et al found that when the expression of Homer1 was downregulated, it inhibited the migration and proliferation of vascular smooth muscle cells (VSMCs) ( 46 , 47 ).…”

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

“…Circular RNAs (circRNAs) are a novel class of long non-coding RNAs, which are widely found in thousands of species of life, including plants, animals and humans, and characterized by covalently closed continuous rings without 5' or 3' polarities structure [26]. Using high-throughput RNA sequencing (RNA-seq) techniques, recent results have shown that a large number of circRNAs are endogenous, stable and widely expressed in mammalian cells, often exhibiting cell type-speci c, tissue-speci c or developmental stage-speci c expression [27][28][29]. There is increasing evidence that some circRNAs may regulate the function of miRNAs, act as miRNA sponges, and play important roles in transcriptional control.…”

Effects of Low-Ambient-Temperature Stimulation on Modifying the Intestinal Structure and Function of Different Pig Breeds

“…MS pig is an excellent indigenous breed in Shanxi Province that is characterized by high fertility, good meat quality, strong resistance to stress and slow growth rate [ 19 , 20 , 21 ]. JFW pig is a local hybrid breed of multiple pigs, including Mashen (6.25%), Taihu (3.13%), Landrace (40.62%) and Yorkshire pigs (50%) [ 22 ].…”