调控山羊绒生长mRNA和lncRNA基因簇及关键信号通路的生物信息学分析

doi:10.16431/j.cnki.1671-7236.2023.11.001

Abstract

Abstract: 【Objective】 The mRNA and lncRNA gene clusters and the key signal pathways that regulated cashmere growth induced by exogenous melatonin of skin in cashmere goats were analyzed, so as to provide a reference for resolving on the molecular mechanism of exogenous melatonin promoting cashmere growth from the perspective of gene clusters.【Method】 Six Hanshan White cashmere goats were selected and randomly assigned to control group and implanted group (melatonin treatment) with three replicates in each group.Take the natural year as the experiment period, skin samples were collected monthly for RNA-Seq analysis.Using Bowtie, TopHat, Cufflinks, Cuffmerge, Cuffdiff, Cuffcompare, CPAT and CPC software to analyze differentially expressed mRNA (DE-mRNA) and differentially expressed lncRNA (DE-lncRNA), Mfuzz package to mine the gene clusters regulating cashmere growth, GSVA and GGally package to analyze the signal pathways regulating cashmere growth.【Result】 A total of 2 024 DE-mRNAs and 329 DE-lncRNAs were identified, which were divided into 8 gene clusters with different dynamic modes in control and melatonin treatment group, respectively.The gene clusters in control group participated in regulating cashmere growth through Hippo signaling pathway, response to interleukin-1, keratin filament, intermediate filament, melanogenesis, cell cycle, FoxO signaling pathway, Wnt signaling pathway, Hh signaling pathway and p53 signaling pathway. The gene clusters in melatonin treatment group participated in regulating cashmere growth through intermediate filament, PI3K-Akt signaling pathway, polymeric cytoskeletal fiber, TGF-beta signaling pathway, growth factor activity, Wnt signaling pathway, Hippo signaling pathway, ECM-receptor interaction, p53 signaling pathway and gap junction.The correlation between DE-mRNA and DE-lncRNA showed that the co-expression network of 55 mRNAs and 10 lncRNAs (PCC>0.960) induced by exogenous melatonin regulating cashmere growth in goats.Gene set variation analysis (GSVA) visualized the dynamic matrix of FoxO, p53, PI3K-Akt, Wnt, Hh, Hippo and TGF-beta signaling pathways regulating cashmere growth at different stages of secondary hair follicle development in skin of cashmere goat.After exogenous melatonin induction, p53 signaling pathway was extremely significantly positively correlated with FoxO signaling pathway (r=0.843, P<0.01).Hh signaling pathway was extremely significantly or significantly positively correlated with Hippo (r=0.836, P<0.01), TGF-beta (r=0.868, P<0.01), Wnt (r=0.790, P<0.01) and PI3K-Akt (r=0.630, P<0.05) signaling pathways.Hippo signaling pathway was extremely significantly or significantly positively correlated with Wnt (r=0.846, P<0.01) and TGF-beta (r=0.806, P<0.05) signaling pathways.Wnt signaling pathway was extremely significantly positively correlated with the TGF-beta signaling pathway (r=0.866, P<0.01).【Conclusion】 The coexpression regulation relationship between 55 mRNAs and 10 lncRNAs regulating cashmere growth in skin of cashmere goats induced by exogenous melatonin had been revealed from the perspective of gene cluster at the omics level, the seven key signaling pathways of FoxO, p53, PI3K-Akt, Wnt, Hh, Hippo and TGF-beta regulating cashmere growth had been identified, which provided a reference for further investigations on the mechanism of melatonin promoting cashmere growth in goats.

Key words: cashmere goat; skin; melatonin; RNA-Seq; gene cluster; signal pathway

CLC Number:

S827

JIA Chunyan, SUN Yanyong, BAO Yonghong, ZHANG Wenguang. Bioinformatics Analysis of mRNA and lncRNA Gene Clusters and Key Signal Pathways Regulating Cashmere Growth[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(11): 4311-4324.

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Bioinformatics Analysis of mRNA and lncRNA Gene Clusters and Key Signal Pathways Regulating Cashmere Growth

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