A genome-wide landscape of mRNAs, lncRNAs, and circRNAs during subcutaneous adipogenesis in pigs

Wei Wei,Shengjuan Wei,Xin Liu,Lifan Zhang,Honglin Liu,Baosen Shan,Jie Chen,Haiyin Han,Kaiqing Liu,Dongfeng Li

doi:10.1186/s40104-018-0292-7

Wei Wei, Shengjuan Wei + Show 8 more

Open Access

https://doi.org/10.1186/s40104-018-0292-7

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Abstract

BackgroundPreadipocyte differentiation plays a critical role in subcutaneous fat deposition in pigs. However, the roles of different RNAs, such as messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in the differentiation process of subcutaneous preadipocytes, are still largely unclear. In the present study, a transcriptome analysis, including the analysis of mRNAs, lncRNAs, and circRNAs, during different differentiation stages, namely, day 0 (D0), day 2 (D2), day 4 (D4), and day 8 (D8), of subcutaneous preadipocytes from Chinese Erhualian pigs was performed.ResultsA total of 1554, 470, 1344, 1777, and 676 differentially expressed (DE) mRNAs, 112, 58, 95, 136, and 93 DE lncRNAs, and 902, 787, 710, 932, and 850 DE circRNAs were identified between D2 and D0, between D4 and D2, between D8 and D4, between D4 and D0, and between D8 and D0, respectively. Furthermore, functional enrichment analysis showed that the common DE mRNAs during the entire differentiation process were mainly involved in lipid metabolic and cell differentiation processes. Additionally, co-expression network analysis identified the potential lncRNAs related to adipogenesis, e.g., MSTRG.131380 and MSTRG.62128.ConclusionsOur study provides new insights of the expression changes of RNAs during adipogenic differentiation, which might contribute to the phenotype of subcutaneous adipogenesis. These results greatly improve our understanding of the molecular mechanisms regulating subcutaneous fat deposition in pigs.

Highlights

Preadipocyte differentiation plays a critical role in subcutaneous fat deposition in pigs
1554, 470, 1344, 1777, and 676 differentially expressed (DE) messenger RNA (mRNA), 112, 58, 95, 136, and 93 DE long non-coding RNAs (lncRNAs), and 902, 787, 710, 932, and 850 DE circRNAs were identified between day 2 (D2) and day 0 (D0), between day 4 (D4) and D2, between day 8 (D8) and D4, between D4 and D0, and between D8 and D0, respectively (Fig. 3d and Additional files 3, 4, 5, 6 and 7)
The results demonstrated that the co-expression network comprised 1328 connections and each lncRNA might correlate with multiple mRNAs (Fig. 6 and Additional file 15)

Summary

Introduction

Preadipocyte differentiation plays a critical role in subcutaneous fat deposition in pigs. The roles of different RNAs, such as messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in the differentiation process of subcutaneous preadipocytes, are still largely unclear. A transcriptome analysis, including the analysis of mRNAs, lncRNAs, and circRNAs, during different differentiation stages, namely, day 0 (D0), day 2 (D2), day 4 (D4), and day 8 (D8), of subcutaneous preadipocytes from Chinese Erhualian pigs was performed. Two main types of noncoding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), have been regarded as key regulators, because they play a vital role in regulating gene expressions at the transcriptional and posttranscriptional levels [4, 5]. Far, the functions of lncRNAs and circRNAs in porcine subcutaneous preadipocyte differentiation are still largely unknown

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