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MSTN-/-牛肌肉miRNA测序及生物信息学分析

miRNA sequencing and bioinformatics analysis of MSTN-/- bovine muscle

  • 摘要: 为了探寻参与调控动物骨骼肌生长发育的肌肉生长抑制素(myostatin, MSTN)基因的相关miRNA,试验活体采集了5头MSTN基因敲除(MSTN-/-)鲁西黄牛(试验组)和5头野生型鲁西黄牛(对照组)的腿臀肌肉,提取肌肉总RNA进行miRNA测序,筛选两组鲁西黄牛肌肉样品间差异表达的miRNA,分析miRNA序列的碱基偏好性,并预测显著差异表达miRNA的靶基因,然后对靶基因进行GO功能和KEGG信号通路富集分析,最后利用实时荧光定量PCR在MSTN基因干扰牛骨骼肌卫星细胞模型上验证miRNA测序数据的准确性。结果表明:miRNA序列第一位碱基的偏好性因长度不同而不同,且不同位置碱基具有偏好性;试验组和对照组样品共鉴定到761个差异表达miRNA,其中有12个显著差异表达miRNA(miR-2285l、miR-496、miR-12006、miR-6533、miR-450b、miR-6524、miR-410、miR-335、miR-2447、miR-147、miR-33a、miR-654),其中试验组有9个较对照组高表达的miRNA(miR-2285l、miR-12006、miR-6533、miR-450b、miR-410、miR-335、miR-147、miR-33a、miR-654)和3个低表达miRNA(miR-496、miR-6524、miR-2447);预测到5 969个显著差异表达miRNA的靶基因和9 280个靶位点;靶基因主要富集在细胞内部、膜结合细胞器、蛋白结合、生物过程的正向调节等相关功能和卡波氏肉瘤病毒感染、胞吞作用、MAPK信号通路等代谢通路;验证试验中的6个miRNA(miR-6533、miR-450b、miR-2285l、miR-654、miR-12006、miR-496)的表达量变化均与测序结果的变化趋势一致。说明12个显著差异表达miRNA可能参与了MSTN基因调控牛骨骼肌生长发育过程。

     

    Abstract: To explore the miRNAs related to the myostatin(MSTN) gens involved in regulating the growth and development of skeletal muscle in animals, the leg and hip muscles of five MSTN knockout(MSTN-/-) Luxi cattle(test group) and five wild-type Luxi cattle(control group) were collected in vivo. Total muscle RNA was extracted for miRNA sequencing, differentially expressed miRNAs in muscle samples between two groups of Luxi cattle were screened, base preference of miRNA sequence was analyzed, and target genes of significantly differentially expressed miRNAs were predicted, and then the target genes were analyzed for gene ontology(GO) function and Kyoto encyclopedia of genes and genomes(KEGG) signaling pathway enrichment. Finally, real-time fluorescence quantitative PCR was utilized to verify the accuracy of the miRNA sequencing data in the satellite cell model of bovine skeletal muscle with MSTN gene interference. The results showed that the preference of the first base of the miRNA sequence was different with the variation of length, and the preference of the base at different positions was different. A total of 761 differentially expressed miRNAs were identified in the test and control samples, including 12 significantly differentially expressed miRNAs(miR-2285l, miR-496, miR-12006, miR-6533, miR-450b, miR-6524, miR-410, miR-335, miR-2447, miR-147, miR-33a, miR-654) in the experimental group. Among them, there were 9 highly expressed miRNAs(miR-2285l, miR-12006, miR-6533, miR-450b, miR-410, miR-335, miR-147, miR-33a, miR-654) and 3 lowly expressed miRNAs(miR-496, miR-6524, miR-2447) in the test group compared to the control group.5 969 target genes and 9 280 target sites of significantly differentially expressed miRNAs were predicted. Target genes are mainly enriched in functions related to intracellular part, membrane-bounded organelle, protein binding, positive regulation of biological process and metabolic pathways such as kaposi’s sarcoma-associated herpesvirus infection, endocytosis and MAPK signaling pathway. The expression changes of all six miRNAs(miR-6533, miR-450b, miR-2285l, miR-654, miR-12006, miR-496) in the validation test were consistent with the trends of the sequencing results. The results indicated that the 12 significantly differentially expressed miRNAs might be involved in MSTN gene regulation of bovine skeletal muscle growth and development.

     

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