| 本文已被：浏览 309次 下载 4402次 |
码上扫一扫！ |
| 外源褪黑素诱导下Hippo信号通路调控山羊绒生长mRNA和lncRNA的生物信息学分析 |
|
贾纯琰1,2,付绍印3,丽春4*,张文广1,5*
|
|
|
| (1.内蒙古农业大学 动物科学学院/内蒙古自治区动物遗传育种与繁殖重点实验室, 呼和浩特 010018;2.内蒙古农业大学 职业技术学院, 内蒙古 包头 014109;3.内蒙古农牧业科学院, 呼和浩特 010031;4.内蒙古民族大学 动物科技学院, 内蒙古 通辽028000;5.内蒙古农业基因组大数据工程研究中心, 呼和浩特 010000) |
|
| 摘要: |
| 为分析绒山羊皮肤中受Hippo信号通路调控的绒生长候选基因集，本研究选取6只罕山白绒山羊随机分为对照组和褪黑素处理组，每组设3个重复。以自然年为试验周期，每月采集皮肤样本进行RNA测序，使用Bowtie、TopHat、Cufflinks、Cuffmerge、Cuffdiff、Cuffcompare、CPAT和CPC软件分析DE-mRNA和DE-lncRNA，联合PCA分析它们对次级毛囊生长周期的应答，利用WGCNA挖掘调控山羊绒生长的基因模块，GSEA分析候选基因集的生物学功能。结果表明:1)筛选得到组间DE-mRNA 2 024个和DE-lncRNA 329个，它们应答了绒山羊皮肤次级毛囊的生长周期。2)获得有生物学意义的对照组7个和试验组9个基因模块。3)深入分析富集到平衡哺乳动物皮肤生长分化、毛囊形态发生的Hippo信号通路基因模块，揭示了外源褪黑素诱导下调控山羊绒生长候选基因集191个mRNA和49个lncRNA的共表达调控网络关系。4)发现候选基因集与皮肤发育生物学过程(|NES|>1且FDR<25%)、Hippo信号通路(|NES|>1且FDR<25%)、Wnt信号通路(|NES|>1且FDR<25%)和细胞周期(|NES|>1且FDR<25%)显著关联。综上，确定了调控山羊绒生长的关键通路Hippo信号通路，在组学水平从基因集角度解析了调控山羊绒生长的mRNA和lncRNA的共表达调控关系，为进一步研究外源褪黑素促山羊绒生长的机制提供参考。 |
| 关键词: 绒山羊皮肤 褪黑素 RNA测序 Hippo信号通路 候选基因集 |
| DOI：10.11841/j.issn.1007-4333.2023.05.12 |
| 投稿时间：2022-07-14 |
| 基金项目:国家自然科学基金项目(31672385)；内蒙古自治区高等学校科学研究项目(NJZY21527) |
|
| Bioinformatics analysis of mRNA and lncRNA induced by exogenous melatonin that regulated cashmere growth by Hippo signaling pathway |
|
JIA Chunyan1,2,FU Shaoyin3,LI Chun4*,ZHANG Wenguang1,5*
|
| (1.Key Laboratory of Animal Genetics and Breeding in Inner Mongolia Autonomous Region/College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China;2.College of Vocational and Technical, Inner Mongolia Agricultural University, Baotou 014109, China;3.Inner Mongolia Agricultural Research Institute, Hohhot 010031, China;4.College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao 028000, China;5.Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010000, China) |
| Abstract: |
| In order to study the cashmere growth candidate gene set that regulated by Hippo signaling pathway in cashmere goat skin. Six Hanshan white cashmere goats were selected and randomly assigned to control group and melatonin treatment group with three replicates in each group. Take the natural year as the experiment period, skin samples were collected monthly for RNA sequencing analysis. Using Bowtie, TopHat, Cufflinks, Cuffmerge, Cuffdiff, Cuffcompare, CPAT and CPC software to analyze differentially expressed mRNA and lncRNA, combined with PCA to analyze that responded to the growth cycle of the secondary hair follicles, WGCNA to mine gene modules regulating cashmere growth, GSEA to analyze the biological functions of candidate gene set. The results showed that: 1)A total of 2 024 differentially expressed mRNAs and 329 differentially expressed lncRNAs were identified, which responded to the growth cycle of the secondary hair follicles in cashmere goat skin. 2)They were divided into 7 and 9 gene modules of biological significance in the control and treatment group. 3)In-depth analysis of Hippo signaling pathway gene module which enriched to balance mammalian skin growth and differentiation and hair follicle morphogenesis. The co-expression network of 191 mRNA and 49 lncRNA in the candidate gene set regulating goat cashmere growth in the treatment group was revealed. 4)The candidate gene set was remarkably related to skin development(|NES|>1 and FDR<25%), Hippo signaling pathway(|NES|>1 and FDR<25%), Wnt signaling pathway(|NES|>1 and FDR<25%)and Cell cycle(|NES|>1 and FDR<25%). In conclusion, the Hippo signaling pathway, a key pathway for regulating cashmere growth, has been identified, and the coexpression regulation relationship between mRNA and lncRNA regulating cashmere growth has been analyzed from the perspective of gene set at the omics level, which provide a reference for further investigations on the mechanism of melatonin promoting cashmere growth in goat. |
| Key words: cashmere goat skin melatonin RNA-seq Hippo signaling pathway candidate gene set |
