Profiling of microRNA in human and mouse ES and iPS cells reveals overlapping but distinct microRNA expression patterns.
Profiling of microRNA in human and mouse ES and iPS cells reveals overlapping but distinct microRNA expression patterns.
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DOI：
10.1371/journal.pone.0073532
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Watanabe S
中科院分区：
文献类型：
--
作者：
Razak SR;Ueno K;Takayama N;Nariai N;Nagasaki M;Saito R;Koso H;Lai CY;Murakami M;Tsuji K;Michiue T;Nakauchi H;Otsu M;Watanabe S
利用基于定量pcr的miRNA阵列，我们全面分析了miRNA在人和小鼠胚胎干细胞（ES）、诱导多能干细胞（iPS）和体细胞中的表达谱。使用SSEA-1或SSEA-4纯化未成熟多能细胞，并用于miRNA分析。如前所述，通过非负矩阵分解的分层聚类和一致聚类显示了人类ES/iPS细胞和其他细胞群两大聚类。主成分分析（PCA）鉴定了在这两组中分离的mirna，鉴定出miR-187、299-3p、499-5p、628-5p和888是特异性表征人类ES/iPS细胞的新mirna。对人类胚胎干细胞和iPS细胞中miRNA表达水平的详细直接比较表明，19号染色体miRNA簇中包含的几种miRNA在iPS细胞中的表达强于在胚胎干细胞中的表达。在小鼠ES/iPS细胞和体细胞中进行了类似的分析，通过PCA发现一些未在小鼠ES/iPS细胞中表达的mirna可能是ES/iPS细胞特异性mirna。比较人和小鼠ES/iPS细胞中miRNAs的平均表达水平，发现人/小鼠miRNAs的表达模式非常相似。然而，一些小鼠或人类特异性mirna被列为高表达。对胚胎体形成过程中miRNA水平的时间轨迹追踪显示其水平变化剧烈且模式不同。总之，我们对人类和小鼠胚胎干细胞和iPS细胞的miRNA表达谱分析为理解调控多能细胞特性的miRNA核心调控网络提供了不同的视角。
Using quantitative PCR-based miRNA arrays, we comprehensively analyzed the expression profiles of miRNAs in human and mouse embryonic stem (ES), induced pluripotent stem (iPS), and somatic cells. Immature pluripotent cells were purified using SSEA-1 or SSEA-4 and were used for miRNA profiling. Hierarchical clustering and consensus clustering by nonnegative matrix factorization showed two major clusters, human ES/iPS cells and other cell groups, as previously reported. Principal components analysis (PCA) to identify miRNAs that segregate in these two groups identified miR-187, 299-3p, 499-5p, 628-5p, and 888 as new miRNAs that specifically characterize human ES/iPS cells. Detailed direct comparisons of miRNA expression levels in human ES and iPS cells showed that several miRNAs included in the chromosome 19 miRNA cluster were more strongly expressed in iPS cells than in ES cells. Similar analysis was conducted with mouse ES/iPS cells and somatic cells, and several miRNAs that had not been reported to be expressed in mouse ES/iPS cells were suggested to be ES/iPS cell-specific miRNAs by PCA. Comparison of the average expression levels of miRNAs in ES/iPS cells in humans and mice showed quite similar expression patterns of human/mouse miRNAs. However, several mouse- or human-specific miRNAs are ranked as high expressers. Time course tracing of miRNA levels during embryoid body formation revealed drastic and different patterns of changes in their levels. In summary, our miRNA expression profiling encompassing human and mouse ES and iPS cells gave various perspectives in understanding the miRNA core regulatory networks regulating pluripotent cells characteristics.
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