Identification and characterization of circular RNAs in Qinchuan cattle testis

Abstract

Circular RNA (circRNA) is a new class of non-coding RNA that has recently attracted researchers' interest. Studies have demonstrated that circRNA can function as microRNA sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in cattle remains unknown. We performed ribo-depleted total RNA-Seq to detect circRNA expression profiles of neonatal (one week old) and adult (4 years old) Qinchuan cattle testes. We obtained 91 112 596 and 80 485 868 clean reads and detected 21 753 circRNAs. A total of 4248 circRNAs were significantly differentially expressed between neonatal and adult cattle testes. Among these circRNAs, 2225 were upregulated, and 2023 were downregulated in adult cattle testis. Genomic feature, length distribution and other characteristics of the circRNAs in cattle testis were studied. Moreover, Gene Ontology and KEGG pathway analyses were performed for source genes of circRNAs. These source genes were mainly involved in tight junction, adherens junction, TGFβ signalling pathway and reproduction, such as PIWIL1, DPY19L2, SLC26A8, IFT81, SMC1B, IQCG and TTLL5. CircRNA expression patterns were validated by RT-qPCR. Our discoveries provide a solid foundation for the identification and characterization of key circRNAs involved in testis development or spermatogenesis.

Mitochondrial Epigenetics: Non-Coding RNAs as a Novel Layer of Complexity

“…In mammalians, there is only limited evidence of mt-circRNAs. Gao et al (2018) found three mt-circRNAs by studying circRNAs expression in cattle testis, but their functions were not elucidated [70]. In mice, it was demonstrated that a nuclear circRNA called MFACR (mitochondrial fission and apoptosis-related circRNA) regulates mitochondrial fission and apoptosis in the heart by regulating miR-652-3p, suggesting that circRNAs are potential biomarkers of cardiovascular diseases [71].…”

The Function of Pre-mRNA Alternative Splicing in Mammal Spermatogenesis

“…Circular RNAs (circRNAs), unlike miRNAs and long non-coding RNAs (lncRNAs), are a novel type of non-coding RNAs originated from introns, intergenic regions, untranslated regions and exhibit distinct patterns of alternative back-splicing and alternative splicing [107,108]. The roles of circRNAs in self-renewal and differentiation of spermatogonial stem cells and sperm motility are gradually being studied [109][110][111][112]. However, the relationships between alternative splicing that involved by circRNAs and spermatogenesis was seldom reported and needed further study.…”

Analysis of Long Non-Coding RNA and mRNA Expression Profiling in Immature and Mature Bovine (Bos taurus) Testes

“…In addition, this organ expresses more complex transcriptomes in comparison with other tissues (Soumillon et al, 2013). Rapid advancement has demonstrated that non-coding RNAs were emerging as important regulators of gene expression at post-transcription in spermatogenesis, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and Piwi-interacting RNA (piRNAs) (Mukherjee et al, 2014; Robles et al, 2017; Gao et al, 2018; Qiu et al, 2018).…”