Background: Preadipocyte 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(c...Background: Preadipocyte 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.Results: A 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.Conclusions: Our 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.展开更多
为探讨系统性硬化症(SSc)患者尿液样本中的长链非编码RNA(lncRNA)、信使RNA(mRNA)的表达谱和生物学功能。选取6名SSc患者和3名健康对照者(HC),采集样本为中段晨尿,应用mRNA和lncRNA微阵列检测总RNA表达变异,SSc组与HC组相比。检测尿液ln...为探讨系统性硬化症(SSc)患者尿液样本中的长链非编码RNA(lncRNA)、信使RNA(mRNA)的表达谱和生物学功能。选取6名SSc患者和3名健康对照者(HC),采集样本为中段晨尿,应用mRNA和lncRNA微阵列检测总RNA表达变异,SSc组与HC组相比。检测尿液lncRNA和mRNA表达,Gene ontology(GO)分析Kyoto Encyclopedia of Genes and Genomes(KEGG)信号通路分析差异表达的lncRNA功能分布;STRING在线网站和Cytoscape软件网络应用分析构建蛋白质相互作用网络(PPI)并筛选出核心基因(Hub Gene)。结果发现:与HC相比,SSc患者尿液中共有645个(上调546,下调99)mRNA和1888个(上调1647,下调241)lncRNA差异表达(Fold Change绝对值≥2,且P≤0.05)。KEGG通路结果显示富集TGF-β信号通路、氧化磷酸化、磷酸戊糖通路。SSc的GO分析显示与转录调控、DNA去甲基化、白介素6反应等相关;PPI网络分析表明主要富集在氧化磷酸化、细胞凋亡、自噬途径通路。通过采用lncRNA基因芯片分析SSc患者尿液样本,发现存在异常表达的lncRNA和mRNA,说明SSc尿液生物学特征与HC组存在差异改变;尿液lncRNA可能可以为该病提供生物标志物及治疗靶点研究方向和手段,尿液线粒体基因可能是SSc生物标记物。展开更多
目的研究中药复方桃红四物汤(Tao Hong Si Wu decoction,THSWD)治疗大脑中动脉闭塞(middle cerebral artery occlusion,MCAO)大鼠长链非编码RNA(long non-coding RNA,lncRNA)的表达,并确定THSWD治疗MCAO大鼠可能的分子机制。方法从对照...目的研究中药复方桃红四物汤(Tao Hong Si Wu decoction,THSWD)治疗大脑中动脉闭塞(middle cerebral artery occlusion,MCAO)大鼠长链非编码RNA(long non-coding RNA,lncRNA)的表达,并确定THSWD治疗MCAO大鼠可能的分子机制。方法从对照组、MCAO组和MCAO+THSWD组各获得3个大脑半球组织。采用RNA测序技术鉴定三组中的lncRNA基因表达。鉴定了THSWD调节的lncRNA基因,然后构建了THSWD调节的lncRNA-mRNA网络。通过MCODE插件鉴定lncRNA-mRNA网络的模块。基因本体(gene ontology,GO)和京都基因与基因组百科全书数据库(kyoto encyclopedia of genes and genomes,KEGG)用于分析富集的生物功能和信号通路。鉴定了THSWD调节的lncRNA的顺式和反式调控基因。采用逆转录实时定量聚合酶链式反应(RT-qPCR)验证lncRNA。分子对接用于验证lncRNA-mRNA网络靶点和通路相关蛋白结合能力。结果在MCAO大鼠中,THSWD共调节了302个lncRNA。生物信息学分析表明,一些核心lncRNA可能在THSWD治疗MCAO大鼠中发挥重要作用,此外,我们进一步发现THSWD可能也通过lncRNA-mRNA网络以及网络富集的补体和凝血级联反应等多通路治疗MCAO大鼠。分子对接结果表明,THSWD活性化合物没食子酸和苦杏仁苷与蛋白质靶点具有一定的结合能力。结论THSWD可以通过调节lncRNA保护MCAO大鼠脑损伤,为THSWD治疗缺血性中风提供了新见解。展开更多
基金supported by the National Transgenic Project of China(2018ZX0800928B)the National Key Technology Research and Development Program of the Ministry of Science and Technology of China(2015BAD03B01)the National Natural Science Foundation of China(31501930)
文摘Background: Preadipocyte 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.Results: A 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.Conclusions: Our 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.
文摘为探讨系统性硬化症(SSc)患者尿液样本中的长链非编码RNA(lncRNA)、信使RNA(mRNA)的表达谱和生物学功能。选取6名SSc患者和3名健康对照者(HC),采集样本为中段晨尿,应用mRNA和lncRNA微阵列检测总RNA表达变异,SSc组与HC组相比。检测尿液lncRNA和mRNA表达,Gene ontology(GO)分析Kyoto Encyclopedia of Genes and Genomes(KEGG)信号通路分析差异表达的lncRNA功能分布;STRING在线网站和Cytoscape软件网络应用分析构建蛋白质相互作用网络(PPI)并筛选出核心基因(Hub Gene)。结果发现:与HC相比,SSc患者尿液中共有645个(上调546,下调99)mRNA和1888个(上调1647,下调241)lncRNA差异表达(Fold Change绝对值≥2,且P≤0.05)。KEGG通路结果显示富集TGF-β信号通路、氧化磷酸化、磷酸戊糖通路。SSc的GO分析显示与转录调控、DNA去甲基化、白介素6反应等相关;PPI网络分析表明主要富集在氧化磷酸化、细胞凋亡、自噬途径通路。通过采用lncRNA基因芯片分析SSc患者尿液样本,发现存在异常表达的lncRNA和mRNA,说明SSc尿液生物学特征与HC组存在差异改变;尿液lncRNA可能可以为该病提供生物标志物及治疗靶点研究方向和手段,尿液线粒体基因可能是SSc生物标记物。
文摘目的研究中药复方桃红四物汤(Tao Hong Si Wu decoction,THSWD)治疗大脑中动脉闭塞(middle cerebral artery occlusion,MCAO)大鼠长链非编码RNA(long non-coding RNA,lncRNA)的表达,并确定THSWD治疗MCAO大鼠可能的分子机制。方法从对照组、MCAO组和MCAO+THSWD组各获得3个大脑半球组织。采用RNA测序技术鉴定三组中的lncRNA基因表达。鉴定了THSWD调节的lncRNA基因,然后构建了THSWD调节的lncRNA-mRNA网络。通过MCODE插件鉴定lncRNA-mRNA网络的模块。基因本体(gene ontology,GO)和京都基因与基因组百科全书数据库(kyoto encyclopedia of genes and genomes,KEGG)用于分析富集的生物功能和信号通路。鉴定了THSWD调节的lncRNA的顺式和反式调控基因。采用逆转录实时定量聚合酶链式反应(RT-qPCR)验证lncRNA。分子对接用于验证lncRNA-mRNA网络靶点和通路相关蛋白结合能力。结果在MCAO大鼠中,THSWD共调节了302个lncRNA。生物信息学分析表明,一些核心lncRNA可能在THSWD治疗MCAO大鼠中发挥重要作用,此外,我们进一步发现THSWD可能也通过lncRNA-mRNA网络以及网络富集的补体和凝血级联反应等多通路治疗MCAO大鼠。分子对接结果表明,THSWD活性化合物没食子酸和苦杏仁苷与蛋白质靶点具有一定的结合能力。结论THSWD可以通过调节lncRNA保护MCAO大鼠脑损伤,为THSWD治疗缺血性中风提供了新见解。
