猪心肌和骨骼肌miRNA转录组比较分析

Comparative analysis on miRNA transcriptomes of cardiac muscle and skeletal muscle in pigs

【目的】研究microRNA(miRNA)在猪不同类型肌肉生长发育中的作用。【方法】以猪心肌以及2种骨骼肌(背最长肌和腰大肌)为材料,采用Illumina高通量测序技术鉴定其miRNA转录组,并进行差异表达分析和靶基因富集分析。【结果】从猪心肌、背最长肌和腰大肌组织的3个小RNA测序文库中共获得约56M的序列,通过生物信息分析共鉴定出907个非冗余miRNA,其中441个miRNA在3个文库共同表达,123个miRNA在文库间表现为显著的差异表达(P<10-6)。对3个文库差异表达miRNA的相关性分析发现,背最长肌与腰大肌的相关性最高(r=0.94),证明2种骨骼肌的表达模式十分相近,而心肌与2种骨骼肌的表达模式不同。通过对各文库高表达的miRNA分析发现,表达量前十的miRNA中有6个miRNA的表达量在心肌中极显著上调。对在心肌内上调的6个miRNA进行的靶基因预测和生物学功能预测发现,这些差异miRNA主要靶向作用于钙信号通路和胰岛素信号通路。荧光定量PCR(qRT-PCR)验证结果表明高通量测序结果准确可靠。【结论】从miRNA层面揭示了猪心肌和骨骼肌的差异,这种差异在一定程度上印证了心肌和骨骼肌之间迥异的生理学特征。

[Objective] This study aimed to understand the function of miRNA in development of dis- tinct muscles in pigs. [Method] Illumina deep sequencing approach was applied for identification of miRNA transcriptomes of cardiac muscle and two skeletal muscles （longissimus dorsi muscle and psoas major muscle） in pigs,and their differential expressions and target genes were analyzed. [Result] A total of 56 million sequences were obtained from three small RNA sequencing libraries and 907 miRNAs were identified, of which 441 were co-expressed and 123 were differentially expressed （P〈10-6） across the three libraries. The correlation analysis of these differentially expressed miRNAs showed that Zongissimus dorsi muscle and psoas major muscle had a similar expression pattern （r=0.94） ,while cardiac muscle had a different expression pattern. By ranking analyses of highly expressed miRNAs in three libraries, six out of the top ten miRNAs in cardiac muscle were up-regulated simultaneously compared to longissimus dorsi muscle and psoas major muscle. GO and KEGG analyses on potentially function of target genes of the six up-regulated miRNAs in cardiac muscle showed that the involved target genes mainly enriched in calcium signaling pathway and insulin signaling pathway, qRT-PCR results also validated the high confidence of the deep sequencing data. [Conclusion] The differences of miRNA transcriptomes in pigs, to some extent, highlighted the dramatically physiological differences between cardiac muscle and skeletal muscles.