Identification and characterization of circular RNAs in Longissimus dorsi muscle tissue from two goat breeds using RNA-Seq

Abstract

Background: Circular RNAs (circRNAs) are a class of non-coding RNA that play crucial roles in the development of skeletal muscle. However, little is known about the role of circRNAs in caprine skeletal muscle. In this study, the muscle ber size and expression pro les of circRNAs were compared in Longissimus dorsi muscle of Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with signi cant phenotypic differences in meat production performance, using hematoxylin and eosin staining and RNA-Seq, respectively.Results: The muscle ber size in LC goats were larger than those in ZB goats (P < 0.05). A total of 10,875 circRNAs were identi ed and 214 of these were differentially expressed between the two caprine breeds.The authentication and expression levels of 20 circRNAs were con rmed using reverse transcriptasepolymerase chain reaction (RT-PCR) and DNA sequencing. The parent genes of differentially expressed circRNAs were mainly enriched in connective tissue development, Rap1, cGMP-PKG, cAMP and Ras signaling pathway. Some miRNAs reportedly associated with skeletal muscle development and intramuscular fat deposition would be targeted by several differentially expressed circRNAs and the most highly expressed circRNA (circ_001086).Conclusion: These results provide an improved understanding of the functions of circRNAs in skeletal muscle development of goats.

Identification and Characterization of Circular RNAs (circRNAs) Using RNA-Seq in Two Breeds of Cashmere Goats

“…However, the number of circRNAs expressed in the study was less than that reported in a previous study of skin tissue in Inner Mongolia cashmere goats at four different embryonic stages, with 21,784 circRNAs being identified [21]. This indicates breed-specific and time-specific expression patterns of circRNAs in goats, which is consistent with previous findings of circRNAs [22][23][24]. In this study, the differential expression of circRNAs also confirmed the breed-specific pattern, as 29 and 50 circRNAs were only expressed in the skin tissue of LC and ZB goats, respectively.…”

Integrated transcriptome analysis reveals roles of long non-coding RNAs (lncRNAs) in caprine skeletal muscle mass and meat quality

“…Brie y, LC goats have higher carcass weight, net meat weight, muscle ber size, and intramuscular fat content, but have poorer meat tenderness compared to ZB goats (P < 0.05) [25]. RNA-Seq analysis of the same Longissimus dorsi muscle tissues as those used in the study revealed that differentially expressed genes, miRNAs and circular RNAs (circRNAs) were responsible for these phenotypic differences [26][27][28]. However, the biological mechanism by lncRNAs regulate meat production performance difference is still unclear.…”

Characteristics and Expression of circ_003628 and Its Promoted Effect on Proliferation and Differentiation of Skeletal Muscle Satellite Cells in Goats

“…With the development of RNA-Seq and bioinformatics technologies, thousands of unique circRNAs have been annotated in skeletal muscle tissues in chickens [ 13 ], cattle [ 14 ], goats [ 15 ], pigs [ 16 ], and sheep [ 17 ]. For example, Lei et al [ 18 ] identified 5755 differentially expressed circRNAs in breast muscle tissue of Shouguang chickens between embryonic periods and postnatal periods.…”

“…For example, Lei et al [ 18 ] identified 5755 differentially expressed circRNAs in breast muscle tissue of Shouguang chickens between embryonic periods and postnatal periods. A total of 214 differentially expressed circRNAs were found in the longissimus dorsi muscle between two goat breeds with different meat yield and quality, and their parent genes were enriched in connective tissue development, Rap1, cGMP-PKG, cAMP and Ras signaling pathway [ 15 ]. These studies confirmed differential expression of circRNAs in skeletal muscle tissues collected from different development periods or different breeds with phenotypic differences in meat production performance.…”

“…In our previous research, circ_003628 was found to be highly expressed with a Reads Per Million mapped reads (RPM; a normalized expression level measure of the circRNA) value of 3228 in the longissimus dorsi muscle of Ziwuling black goats [ 15 ]. This suggests that circ_003628 may be important for muscle growth and development.…”