Integrative analysis of circRNAs, miRNAs, and mRNAs profiles to reveal ceRNAs networks in chicken intramuscular and abdo
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RESEARCH ARTICLE
Open Access
Integrative analysis of circRNAs, miRNAs, and mRNAs profiles to reveal ceRNAs networks in chicken intramuscular and abdominal adipogenesis Meng Zhang1, Yu Han2, Yanhui Zhai1, Xiangfei Ma3, Xinglan An1, Sheng Zhang1* and Ziyi Li1*
Abstract Background: Tissue-specific fat deposition is regulated by a series of complex regulatory mechanisms. Reports indicate that epigenetic regulators, such as circular RNAs (circRNAs), are crucial in diseases progression, animal development, metabolism, and adipogenesis. In this study, to assess the functional roles of circRNAs in adipogenesis and tissue-specific fat deposition, we comprehensively analyzed the Ribo-Zero RNA-Seq and miRNAs data during chicken intramuscular and abdominal adipogenic differentiation. Results: circRNAs and miRNAs profiles during chicken adipogenic differentiation were found in adipocytes derived from various adipose tissues. It was also discovered that high levels of downregulated miRNAs potentially promote adipogenesis by activating their target genes which are associated with fatty acid metabolism and adipogenic differentiation. Through analysis of the correlation between the expression levels of circRNAs and adipogenic genes, as well as the dynamic expression patterns of circRNAs during adipogenic differentiation, several candidate circRNAs were identified. Moreover, competing endogenous RNA (ceRNAs) networks were constructed during chicken intramuscular and abdominal adipogenesis by combining miRNAs with mRNAs data. Several candidate circRNAs potentially influence adipogenesis by regulating miRNAs via PPAR and fatty acid metabolism-related pathways were identified, such as circLCLAT1, circFNDC3AL, circCLEC19A and circARMH1. Conclusion: In conclusion, our findings reveal that circRNAs and the circRNA-miRNAs-mRNAs-ceRNAs network may play important roles in chicken adipocytes differentiation and tissue-specific fat deposition. Keywords: Chicken, circRNAs, ceRNA, Intramuscular fat, Abdominal fat, Adipogenic differentiation
Background Different resources and organizational microenvironment dictate various physiological and biochemical characteristics of adipose tissues [1–3]. Since preadipocytes derived from various tissues exhibit distinct proliferation speed and adipogenic potential, it is believed that * Correspondence: [email protected]; [email protected] 1 Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun 130021, Jilin, China Full list of author information is available at the end of the article
transcriptional and post-transcriptional regulation mechanisms cause stage- and tissue-specific fat deposition in animals [4–6]. An increasing number of studies have shown that noncoding RNAs regulates various normal and pathological processes, such as microRNAs (miRNAs) [7–10] and long noncoding RNAs (lncRNAs) [11–13]. Although recent studies on the role of miRNAs and lncRNAs in adipogenesis have reached a mature stage, information on the functiona
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