Identification of lncRNA-miRNA-mRNA Network Involved in Sexual Size Dimorphism of Chinese Tongue Sole (Cynoglossus semilaevis)
Identification of lncRNA-miRNA-mRNA Network Involved in Sexual Size Dimorphism of Chinese Tongue Sole (Cynoglossus semilaevis)
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DOI：
10.3389/fmars.2022.795525
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发表时间：
2022-02
期刊：
影响因子：
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通讯作者：
Jialin Wang;Qiang Yang;Yuanri Hu;Wen‐teng Xu;Yingming Yang;Songlin Chen;Na Wang
中科院分区：
文献类型：
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作者：
Jialin Wang;Qiang Yang;Yuanri Hu;Wen‐teng Xu;Yingming Yang;Songlin Chen;Na Wang
半滑舌鳎（Cynoglossus semilaevis）是东北亚特有的一种比目鱼，具有典型的雌性偏好性大小二型性（SSD）。为了探讨非编码RNA（ncRNA）在这一现象中的可能调控作用，我们用雌性、雄性和假单胞菌C. semilaevis用于识别来自大脑、性腺、肝脏和肌肉组织的差异表达（DE）长ncRNA（DE lncRNA）、微小RNA（DE miRNA）以及差异表达基因（DEG）。其中大部分集中在性腺和肌肉中，假单胞菌个体的基因表达模式与雄性个体相似。基于反义、顺式和反式调节机制预测DE lncRNA和靶信使RNA（mRNA）的关联，具有富集的蛋白质消化和吸收、环磷酸腺苷（cAMP）信号通路、硫代谢、细胞周期和剪接体（p < 0.05）。利用加权基因共表达网络分析（WGCNA）对DE lncRNA的表达模式进行聚类分析，结果表明，有两个模块（绿黄和蓝色）分别与生长性状呈正相关和负相关。重要的是，在性腺中观察到黄绿色模块中的雌性偏好表达以及蓝色模块中的雄性和假雄性偏好表达。DE miRNA的靶基因分析显示了3，034个具有相反表达模式的mRNA-miRNA对。最终构建了包括385个DE lncRNA、138个DE miRNAs和456个DEG的lncRNA-miRNAs-mRNA网络。其中78个DE lncRNAs、12个DE miRNAs和13个DEGs参与了细胞生长和死亡途径，与C.半滑鱼本研究描述了C.第一次见到半人半兽。功能预测分析表明，这些DE lncRNA和DE miRNAs可能通过调节几种潜在的生长相关途径（例如，细胞周期、cAMP信号传导和Rap 1信号传导）。对这些ncRNA的进一步研究将加深我们对ncRNA对鱼类SSD调控作用的理解。
Chinese tongue sole (Cynoglossus semilaevis) is a flatfish species unique to Northeast Asia, exhibiting the typical female-biased sexual size dimorphism (SSD). To explore the possible regulatory roles of non-coding RNAs (ncRNAs) on this phenomenon, whole transcriptomic analysis was performed by using female, male, and pseudomale C. semilaevis to identify differentially expressed (DE) long ncRNAs (DE lncRNAs), microRNA (DE miRNAs), and differentially expressed genes (DEGs) from the brain, gonad, liver, and muscle tissues. Most of them were concentrated in the gonad and muscle, and the gene expression patterns of pseudomale individuals were similar to male individuals. The association of DE lncRNAs and target messenger RNAs (mRNAs) was predicted based on antisense, cis-, and trans-regulatory mechanisms, with enriched protein digestion and absorption, cyclic adenosine monophosphate (cAMP) signaling pathway, sulfur metabolism, cell cycle, and splicesome (p < 0.05). Furthermore, weighted gene co-expression network analysis (WGCNA) was employed to cluster the expression patterns of DE lncRNA, and two modules (greenyellow and blue) had the highest positive and negative correlations with growth traits, respectively. Importantly, the female-biased expression in the greenyellow module and the male- and pseudomale-biased expression in the blue module were observed in the gonad. The target gene analysis for DE miRNA revealed 3,034 mRNA-miRNA pairs with the opposite expression patterns. Finally, the lncRNA-miRNA-mRNA network, including 385 DE lncRNAs, 138 DE miRNAs, and 456 DEGs, was constructed. Among which, 78 DE lncRNAs, 12 DE miRNAs, and 13 DEGs involved in cell growth and death pathway were related to the SSD of C. semilaevis. This study described the lncRNA-miRNA-mRNA regulatory network in the SSD of C. semilaevis for the first time. The functional prediction analysis suggested that these DE lncRNAs and DE miRNAs might be involved in flatfish SSD by regulating several potential growth-related pathways (e.g., cell cycle, cAMP signaling, and Rap1 signaling). Further studies related to these ncRNAs will enlarge our understanding of the regulatory effects of ncRNAs on fish SSD.