Identification of circular RNAs in the ovarian follicles of Meishan and Duroc sows during the follicular phase
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RESEARCH
Open Access
Identification of circular RNAs in the ovarian follicles of Meishan and Duroc sows during the follicular phase Su Xie1†, Mengxun Li1,2†, Yansen Chen3, Yi Liu1, Lipeng Ma1, Xiaomei Sun1, Yishan Sun1, Ruonan Gao1 and Tao Huang1*
Abstract Circular RNAs (circRNAs) are a newly discovered class of endogenous non-coding RNAs that play an important role in growth and development by regulating gene expression and participating in a variety of biological processes. However, the role of circRNAs in porcine follicles remains unclear. Therefore, this study examined middle-sized ovarian follicles obtained from Meishan and Duroc sows at day 4 of the follicular phase. High-throughput RNA sequencing (RNA-seq) was utilized to construct circRNAs, and differential expression was identified. The findings were validated using reverse transcription PCR (RT-PCR) and DNA sequencing, GO and KEGG analyses were performed, and potential miRNA targets were identified. The RNA-seq identified a total of 15,866 circRNAs, with 244 differentially expressed in the Meishan relative to the Duroc (111 up-regulated and 133 down-regulated). The RT-PCR finding confirmed the RNA-seq results, and quantitative real-time PCR (qPCR) analysis examining a subset of the circRNAs showed that they are resistant to RNase R digestion. Bioinformatics analysis (GO and KEGG) showed that the host genes associated with the differentially expressed circRNAs are involved in reproduction and follicular development signaling pathways. Furthermore, many of the circRNAs were found to interact with miRNAs that are associated with follicular development. This study presents a new perspective for studying circRNAs and provides a valuable resource for further examination into the potential roles of circRNAs in porcine follicular development. Keywords: Middle-sized ovarian follicles, Sows, Circular RNAs, Follicular phase, Meishan
Introduction For the past few years, circular RNAs (circRNAs) have attracted attention as a new member of the noncoding RNA family in animals [1–3]. In 1976, Sanger et al. first discovered that certain higher plant viruses were covalently closed circular RNA molecules [4]. Then in 1986, Kos et al. discovered that the hepatitis delta virus (HDV) genome comprises circRNA [5]. In recent years, breakthroughs in high-throughput deep sequencing * Correspondence: [email protected] † Su Xie and Mengxun Li contributed equally to this work. 1 College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi 832000, China Full list of author information is available at the end of the article
technology have identified circRNAs in humans [3, 6, 7], mice [6, 7], nematodes [7, 8] and coelacanths [9]. Furthermore, studies have shown that circRNAs exhibit specific expression patterns in different tissues or cell types and at different developmental stages [3, 7]. The richness and diversity of circRNA expression may be related to the alternative splicing of RNA transcripts. Moreover, circRNA formation is facilitated by t
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