基于转录组学分析受外源褪黑素诱导调控羊绒生长的mRNA和lncRNA的可变剪接

doi:10.16431/j.cnki.1671-7236.2025.07.018

Abstract

Abstract: 【Objective】 This study was aimed to analyze mRNA and long non-coding RNA (lncRNA) in cashmere goat skin induced by exogenous melatonin to participate in the regulation of alternative splicing (AS) of cashmere growth at post transcriptional level,so as to provide a reference for exploring the effect of AS regulation on melatonin promoting cashmere growth in goats. 【Method】 Six Hanshan White cashmere goats were selected and randomly assigned to control and implant groups with three replicates in each group.Take the natural year as the experiment period,skin samples were collected monthly for RNA-Seq analysis.UsedBowtie,TopHat,Cufflinks,Cuffmerge,Cuffdiff,Cuffcompare,CPAT and CPC software were used to analyze differentially expressed mRNA (DE-mRNA) and differentially expressed lncRNA (DE-lncRNA),with rMATS software to identify differential alternative splicing events (DASE) of mRNA and lncRNA in cashmere goat skin transcriptome. 【Result】 The number of DE-mRNA (FDR≤0.05) between the two groups from January to December was 23,93,43,652,1 178,194,353,357,435,36,55 and 52,respectively.The number of DE-lncRNA (FDR≤0.05) between the two groups from January to December was 15,20,10,40,191,50,63,33,79,7,9 and 5,respectively.The number of DASE between the two groups involving mRNA and lncRNA was 715 and 569,respectively.Skipping exon (SE) and mutually exclusive exons (MXE) were the main alternative splicing ways of mRNA.SE,retained intron (RI) and alternative 3'-splice site (A3SS) were the main AS ways of lncRNA.The top 3 chromosomes of DASE number in mRNA were Chr1,Chr5 and Chr10/Chr11 (juxtaposition),and the top 3 chromosomes of DASE in lncRNA were Chr1,Chr19 and Chr10,respectively.Two or more splicing isoforms of mRNA and lncRNA were found in cashmere goat skin.A total of 443 DAS-mRNA and 271 DAS-lncRNA were identified.The top 3 months of DAS-mRNA distribution were October,June and May,and the top 3 months of DAS-lncRNA distribution were May，April and August,respectively.A total of 67 DE-mRNA and 7 DE-lncRNA underwent DASE.The AS regulatory network induced by exogenous melatonin，which composed of 334 DE-mRNA and 8 DE-lncRNA associated with mRNA and lncRNA underwent AS of Pearson’s correlation coefficient (PCC) ranking in top 10 (PCC＞0.800). 【Conclusion】 There were abundant ASE in cashmere goat skin,except for SE,mRNA preferred the alternative splicing way of MXE,while lncRNA preferred RI.Compared with mRNA,the distribution of DASE in lncRNA on chromosomes was specific.When induced by exogenous melatonin,the cashmere fast-growing and the early growth period were main periods for mRNA,while the early growth and the growth period were the main periods for lncRNA occurrence of AS.The potential interaction network between DE-mRNA and DE-lncRNA involved in the transcriptome of cashmere goat skin undergoing AS was constructed,DE-mRNA and DE-lncRNA participated in regulating cashmere growth through AS at the post transcriptional level,providing a reference for further exploring the effect of AS regulation on melatonin promoting cashmere growth.

Key words: cashmere goat; skin; melatonin; RNA-Seq; lncRNA; AS

CLC Number:

S813.3

JIA Chunyan, SUN Yanyong, BAO Yonghong, ZHANG Wenguang, DU Chenguang. Alternative Splicing Analysis of mRNA and lncRNA Induced by Exogenous Melatonin for Regulating Cashmere Growth Based on Transcriptomics[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(7): 3165-3177.

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Alternative Splicing Analysis of mRNA and lncRNA Induced by Exogenous Melatonin for Regulating Cashmere Growth Based on Transcriptomics

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