Integrated lncRNA and mRNA Transcriptome Analyses in the Ovary of Cynoglossus semilaevis Reveal Genes and Pathways Potentially Involved in Reproduction.
Integrated lncRNA and mRNA Transcriptome Analyses in the Ovary of Cynoglossus semilaevis Reveal Genes and Pathways Potentially Involved in Reproduction.
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半滑舌鱼卵巢中的综合 lncRNA 和 mRNA 转录组分析揭示了可能参与繁殖的基因和途径
DOI：
10.3389/fgene.2021.671729
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发表时间：
2021
影响因子：
3.7
通讯作者：
Shi B
中科院分区：
文献类型：
--
作者：
Dong Y;Lyu L;Zhang D;Li J;Wen H;Shi B
据报道，长链非编码rna （lncRNAs）参与了多种生物过程。然而，lncrna在半光滑舌鳎（Cynoglossus semilaevis）繁殖中的作用尚不清楚，特别是在驱动卵巢发育和排卵的分子调控机制方面。因此，为了探索调节生殖的mRNA和lncRNA机制，我们采集了舌底卵巢的三个阶段进行RNA测序。在IV期和V期，我们鉴定了312个差异表达（DE） mrna和58个DE lncrna。在V期和VI期，我们鉴定了1,059个DE mrna和187个DE lncrna。基因本体（GO）和京都基因与基因组百科全书（KEGG）富集分析显示，DE mrna在ecm受体相互作用、卵母细胞减数分裂和类固醇激素生物合成途径中富集。此外，我们还进行了基因集富集分析（GSEA），以确定潜在的生殖相关途径，如脂肪代谢和视黄醇代谢。在富集分析的基础上，我们选择了在生殖中具有潜在作用的DE mrna，并将其分为6类，包括信号转导、细胞生长与死亡、免疫应答、代谢、运输与分解代谢以及细胞连接。根据反义、顺式和反式调节机制预测DE lncrna和mrna的相互作用。我们构建了一个竞争性的内源性RNA （ceRNA）网络。预计有几种lncrna调节与生殖相关的基因，包括cyp17a1、cyp19a1、mmp14、pgr和hsd17b1。对这些lncRNAs靶基因的功能富集分析表明，它们参与了tgf - β、Wnt、MAPK等信号通路和孕激素介导的卵母细胞成熟、卵母细胞减数分裂、GnRH等生殖相关信号通路。RT-qPCR分析显示，两个lncRNAs （XR_522278.2和XR_522171.2）主要在卵巢中表达。双荧光原位杂交实验表明，XR_522278.2和XR_522171.2分别在滤泡细胞层与靶基因cyp17a1和cyp19a1共定位。结果进一步证明lncRNAs可能通过调控基因表达参与了生物过程。综上所述，本研究提供了舌底卵巢的lncRNA图谱，并进一步了解了lncRNA参与调节舌底生殖的作用。
Long non-coding RNAs (lncRNAs) have been reported to be involved in multiple biological processes. However, the roles of lncRNAs in the reproduction of half-smooth tongue sole (Cynoglossus semilaevis) are unclear, especially in the molecular regulatory mechanism driving ovarian development and ovulation. Thus, to explore the mRNA and lncRNA mechanisms regulating reproduction, we collected tongue sole ovaries in three stages for RNA sequencing. In stage IV vs. V, we identified 312 differentially expressed (DE) mRNAs and 58 DE lncRNAs. In stage V vs. VI, we identified 1,059 DE mRNAs and 187 DE lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that DE mRNAs were enriched in ECM-receptor interaction, oocyte meiosis and steroid hormone biosynthesis pathways. Furthermore, we carried out gene set enrichment analysis (GSEA) to identify potential reproduction related-pathways additionally, such as fatty metabolism and retinol metabolism. Based on enrichment analysis, DE mRNAs with a potential role in reproduction were selected and classified into six categories, including signal transduction, cell growth and death, immune response, metabolism, transport and catabolism, and cell junction. The interactions of DE lncRNAs and mRNAs were predicted according to antisense, cis-, and trans-regulatory mechanisms. We constructed a competing endogenous RNA (ceRNA) network. Several lncRNAs were predicted to regulate genes related to reproduction including cyp17a1, cyp19a1, mmp14, pgr, and hsd17b1. The functional enrichment analysis of these target genes of lncRNAs revealed that they were involved in several signaling pathways, such as the TGF-beta, Wnt signaling, and MAPK signaling pathways and reproduction related-pathways such as the progesterone-mediated oocyte maturation, oocyte meiosis, and GnRH signaling pathway. RT-qPCR analysis showed that two lncRNAs (XR_522278.2 and XR_522171.2) were mainly expressed in the ovary. Dual-fluorescence in situ hybridization experiments showed that both XR_522278.2 and XR_522171.2 colocalized with their target genes cyp17a1 and cyp19a1, respectively, in the follicular cell layer. The results further demonstrated that lncRNAs might be involved in the biological processes by modulating gene expression. Taken together, this study provides lncRNA profiles in the ovary of tongue sole and further insight into the role of lncRNA involvement in regulating reproduction in tongue sole.
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影响因子：
64.8
作者：
Carrieri, Claudia;Cimatti, Laura;Gustincich, Stefano
通讯作者：
Gustincich, Stefano
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
视黄酸稳态通过 aldh1a2 和 cyp26a1 介导尼罗罗非鱼 (Oreochromis niloticus) 的减数分裂进入
影响因子：
4.6
作者：
Feng R;Fang L;Cheng Y;He X;Jiang W;Dong R;Shi H;Jiang D;Sun L;Wang D
通讯作者：
Wang D
影响因子：
12.4
作者：
De Cian, Marie-Cecile;Gregoire, Elodie P.;Chaboissier, Marie-Christine
通讯作者：
Chaboissier, Marie-Christine
DOI：
10.1016/j.cbpb.2016.03.006
发表时间：
2016-08-01
影响因子：
2.2
作者：
Liu, Jinxiang;Zhang, Wei;Wang, Xubo
通讯作者：
Wang, Xubo