MT和FGF5调控辽宁绒山羊绒毛生长相关LncRNA的筛选及鉴定
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摘要
【目的】筛选出辽宁绒山羊皮肤成纤维细胞中与绒毛生长相关的LncRNA,为绒毛生长相关LncRNA的功能及机制研究提供基础性数据。【方法】提取MT和FGF5处理的辽宁绒山羊皮肤成纤维细胞总RNA,通过样品总RNA电泳检测、测序数据质量评估、Mapping比对、样品间相关性检查对提取的总RNA进行质量检测。筛选出差异表达的LncRNA并预测其靶基因,通过GO和KEGG富集分析,筛选出与绒毛生长相关的LncRNA,并通过Real-time PCR对目标LncRNA进行表达验证。【结果】(1)样品总RNA质量检测结果显示:RNA完整性良好、GC含量相对较高,序列较稳定、样品间表达水平相关性均较高、符合测序要求。(2)差异表达LncRNA的筛选结果显示:1.0g·L~(-1) 24h组差异表达LncRNA有32个,其中4个表达上调,28个表达下调;0.2g·L~(-1) 24h组差异表达LncRNA有10个,其中4个表达上调,6个表达下调;0.2g·L~(-1) 72h组差异表达LncRNA有113个,其中5个表达上调,108个表达下调。10~(-4) g·L~(-1) 24 h组差异表达LncRNA有164个,其中有70个上调,94个下调;10~(-4)g·L~(-1) 72 h差异表达LncRNA有189个,其中有78个上调,111个下调;10~(-6) g·L~(-1) 24 h组差异表达的LncRNA有123个,其中有27个上调,96个下调。(3)靶基因GO富集分析结果显示:1.0g·L~(-1) 24h组差异表达LncRNA靶基因富集在GO的negative regulation of transcription from RNA polymerase Ⅱ promoter;0.2g·L~(-1) 24h组无差异表达LncRNA靶基因富集的GO term;0.2g·L~(-1) 72h组差异表达LncRNA靶基因富集在GO的cellular metabolicprocess biological_process,binding molecular_function,FGF5处理组中只有10~(-4) g·L~(-1) 72 h组差异表达LncRNA靶基因富集在cell cellular_component、cell part cellular_component、intracellular cellular_component、binding molecular_function等6个条目。(4)靶基因KEGG富集分析结果显示:1.0g·L~(-1) 24h组差异表达LncRNA靶基因富集在Steroid biosynthesis pathway;0.2g·L~(-1) 24h组无差异表达LncRNA靶基因富集的Pathway term;0.2g·L~(-1) 72h组差异表达LncRNA靶基因富集在Cell cycle,DNA replication,Steroid biosynthesis,TNF,Nod-likereceptor,NF-kappa B等信号通路,其中TNF和NF-kappa B信号通路与绒毛生长相关。FGF5处理组中,10~(-4) g·L~(-1)72 h组差异表达的LncRNA靶基因显著富集到Fanconi anemia pathway,Huntington's disease,Metabolic pathway,Aminoacyl-tRNA biosynthesis等9个pathway term,其中Metabolic信号通路与绒毛生长相关;10~(-4) g·L~(-1) 24 h组差异表达的LncRNA靶基因无显著富集的pathway term;10~(-6) g·L~(-1) 24 h组差异表达的LncRNA靶基因只富集在Taste transduction pathway。(5)NF-κB和TNF两个信号通路中富集的靶基因TNFα、TNFAIP3(A20)、NFKBIA(IkBα)、NFKB2、IL8所对应的LncRNA有2个,分别为(Gene ID):XLOC_005914;XLOC_018763;Metabolic信号通路中靶基因所对应的LncRNA有4个,分别为(Gene ID):XLOC_011424、XLOC_009522、XLOC_009063、XLOC_01115。Real-time PCR结果显示:LncRNA XLOC_011424、XLOC_011157、LncRNA XLOC_005914和XLOC_018763与高通量测序结果一致。【结论】LncRNA XLOC_011424、XLOC_011157、LncRNA XLOC_005914和XLOC_018763可能通过调控与绒毛生长相关的NF-κB、TNF或Metabolic信号通路,提高羊绒密度和长度,进而提高辽宁绒山羊绒产量及品质。
【Objective】 The aim of this study was to screen out the LncRNA associated with villus growth in Liaoning cashmere goat skin fibroblasts, and provide basic data for the study of the function and mechanism of LncRNA related to villus growth. 【Method】 The total RNA of MT and FGF5 treated Liaoning cashmere goat skin fibroblasts was extracted, and the total RNA extracted was detected by total RNA electrophoresis detection, sequencing data quality evaluation, mapping comparison and inter-sample correlation test. The differentially expressed LncRNA was screened and its target gene was predicted. The LncRNA related to villus growth was screened by GO and KEGG enrichment analysis, and the target LncRNA was verified by Real-time PCR. 【Result】(1) The total RNA quality of the sample showed that the RNA was in good integrity, the GC content was relatively high, the sequence was stable, and the expression level between samples was high, which met the sequencing requirements.(2)Screening of differentially expressed LncRNA showed that there were 32 differentially expressed LncRNA in 1.0 g·L~(-1) 24 h group, 4 of which were up-regulated and 28 of which were down-regulated. There were 10 differentially expressed LncRNA in 0.2 g·L~(-1) 24 h group, 4 of which were up-regulated and 6 were down-regulated. There were 113 differentially expressed LncRNA in the 0.2 g·L~(-1)72 h group, of which 5 were up-regulated and 108 were down-regulated. There were 164 differentially expressed LncRNA in the10~(-4) g·L~(-1) 24 h group, of which 70 were up-regulated and 94 were down-regulated. There were 189 differentially expressed LncRNA in the10~(-4) g·L~(-1) 72 h group, of which 78 were up-regulated and 111 were down-regulated. There were 123 LncRNA differentially expressed in the 10~(-6) g·L~(-1) 24 h group, among which 27 up and 96 down.(3) Target gene GO enrichment analysis showed that the 1.0 g·L~(-1) 24 h group differentially expressed LncRNA target gene enrichment in GO's negative regulation of transcription from RNA polymerase Ⅱ promoter; 0.2 g·L~(-1) 24 h group did not differentially express LncRNA target gene enriched GO term;0.2 g·L~(-1) 72 h group Differentially expressed LncRNA target gene enrichment in GO's cellular metabolic process biological_process, binding molecular_function, FGF5 treatment group only10~(-4) g·L~(-1) 72 h group differentially expressed LncRNA target gene enriched in cell cellular_component, cell part cellular_component, intracellular cellular_component, binding molecular_function and other six items.(4) Target gene KEGG enrichment analysis showed that the differential expression of LncRNA target gene in 1.0 g·L~(-1) 24 h group was enriched in Steroid biosynthesis pathway; in 0.2 g·L~(-1) 24 h group, there was no differential expression of LncRNA target gene enrichment Pathway term; 0.2 g·L~(-1) 72 h group differentially expressed LncRNA target gene enrichment in Cell cycle, DNA replication, Steroid biosynthesis, TNF, Nod-like receptor, NF-kappa B and other signaling pathways, in which TNF and NF-kappa B signaling pathways are involved in villus growth. In FGF5-treated group,differentially expressed LncRNA targets in 10~(-4) g·L~(-1) 72 h group The gene was significantly enriched into nine path termes such as Fanconi anemia pathway, Huntington's disease, Metabolic pathway, Aminoacyl-tRNA biosynthesis, among which Metabolic pathway was associated with villus growth; the differentially expressed LncRNA target gene in 10~(-4) g·L~(-1) 24 h group had no significant enriched pathway term;10~(-6) g·L~(-1) 24 h The differentially expressed LncRNA target genes were only enriched in the Taste transduction pathway.(5) There are two LncRNA corresponding to the target genes TNFα, TNFAIP3(A20), NFKBIA(IkBα), NFKB2 and IL8 enriched in NF-κB and TNF signaling pathways, respectively(Gene ID): XLOC_005914; XLOC_018763;There are four LncRNA corresponding to the target genes in the Metabolic pathway, namely(Gene ID): XLOC_011424,XLOC_009522, XLOC_009063, XLOC_01115. Real-time PCR results showed that LncRNA XLOC_011424, XLOC_011157,LncRNA XLOC_005914 and XLOC_018763 were consistent with high-throughput sequencing results. 【Conclusion】 LncRNA XLOC_011424, XLOC_011157, LncRNA XLOC_005914 and XLOC_018763 may increase the density and length of cashmere by regulating NF-κB, TNF or Metabolic signaling pathways related to villus growth, and thus improve the yield and quality of cashmere in Liaoning cashmere goat.
【Objective】 The aim of this study was to screen out the LncRNA associated with villus growth in Liaoning cashmere goat skin fibroblasts, and provide basic data for the study of the function and mechanism of LncRNA related to villus growth. 【Method】 The total RNA of MT and FGF5 treated Liaoning cashmere goat skin fibroblasts was extracted, and the total RNA extracted was detected by total RNA electrophoresis detection, sequencing data quality evaluation, mapping comparison and inter-sample correlation test. The differentially expressed LncRNA was screened and its target gene was predicted. The LncRNA related to villus growth was screened by GO and KEGG enrichment analysis, and the target LncRNA was verified by Real-time PCR. 【Result】(1) The total RNA quality of the sample showed that the RNA was in good integrity, the GC content was relatively high, the sequence was stable, and the expression level between samples was high, which met the sequencing requirements.(2)Screening of differentially expressed LncRNA showed that there were 32 differentially expressed LncRNA in 1.0 g·L~(-1) 24 h group, 4 of which were up-regulated and 28 of which were down-regulated. There were 10 differentially expressed LncRNA in 0.2 g·L~(-1) 24 h group, 4 of which were up-regulated and 6 were down-regulated. There were 113 differentially expressed LncRNA in the 0.2 g·L~(-1)72 h group, of which 5 were up-regulated and 108 were down-regulated. There were 164 differentially expressed LncRNA in the10~(-4) g·L~(-1) 24 h group, of which 70 were up-regulated and 94 were down-regulated. There were 189 differentially expressed LncRNA in the10~(-4) g·L~(-1) 72 h group, of which 78 were up-regulated and 111 were down-regulated. There were 123 LncRNA differentially expressed in the 10~(-6) g·L~(-1) 24 h group, among which 27 up and 96 down.(3) Target gene GO enrichment analysis showed that the 1.0 g·L~(-1) 24 h group differentially expressed LncRNA target gene enrichment in GO's negative regulation of transcription from RNA polymerase Ⅱ promoter; 0.2 g·L~(-1) 24 h group did not differentially express LncRNA target gene enriched GO term;0.2 g·L~(-1) 72 h group Differentially expressed LncRNA target gene enrichment in GO's cellular metabolic process biological_process, binding molecular_function, FGF5 treatment group only10~(-4) g·L~(-1) 72 h group differentially expressed LncRNA target gene enriched in cell cellular_component, cell part cellular_component, intracellular cellular_component, binding molecular_function and other six items.(4) Target gene KEGG enrichment analysis showed that the differential expression of LncRNA target gene in 1.0 g·L~(-1) 24 h group was enriched in Steroid biosynthesis pathway; in 0.2 g·L~(-1) 24 h group, there was no differential expression of LncRNA target gene enrichment Pathway term; 0.2 g·L~(-1) 72 h group differentially expressed LncRNA target gene enrichment in Cell cycle, DNA replication, Steroid biosynthesis, TNF, Nod-like receptor, NF-kappa B and other signaling pathways, in which TNF and NF-kappa B signaling pathways are involved in villus growth. In FGF5-treated group,differentially expressed LncRNA targets in 10~(-4) g·L~(-1) 72 h group The gene was significantly enriched into nine path termes such as Fanconi anemia pathway, Huntington's disease, Metabolic pathway, Aminoacyl-tRNA biosynthesis, among which Metabolic pathway was associated with villus growth; the differentially expressed LncRNA target gene in 10~(-4) g·L~(-1) 24 h group had no significant enriched pathway term;10~(-6) g·L~(-1) 24 h The differentially expressed LncRNA target genes were only enriched in the Taste transduction pathway.(5) There are two LncRNA corresponding to the target genes TNFα, TNFAIP3(A20), NFKBIA(IkBα), NFKB2 and IL8 enriched in NF-κB and TNF signaling pathways, respectively(Gene ID): XLOC_005914; XLOC_018763;There are four LncRNA corresponding to the target genes in the Metabolic pathway, namely(Gene ID): XLOC_011424,XLOC_009522, XLOC_009063, XLOC_01115. Real-time PCR results showed that LncRNA XLOC_011424, XLOC_011157,LncRNA XLOC_005914 and XLOC_018763 were consistent with high-throughput sequencing results. 【Conclusion】 LncRNA XLOC_011424, XLOC_011157, LncRNA XLOC_005914 and XLOC_018763 may increase the density and length of cashmere by regulating NF-κB, TNF or Metabolic signaling pathways related to villus growth, and thus improve the yield and quality of cashmere in Liaoning cashmere goat.
引文
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[5]YU F,LIU Z,JIAO S,ZHANG X,BAI C,ZHANG J,YAN S.Anonsense mutation in the FGF5 gene is associated with the longhaired phenotype in domestic guinea pigs(Cavia porcellus).Animal Genetics,2018,49(3):269.
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