miRNA arm selection and isomiR distribution in gastric cancer.
miRNA arm selection and isomiR distribution in gastric cancer.
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DOI：
10.1186/1471-2164-13-s1-s13
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发表时间：
2012
期刊：
影响因子：
4.4
通讯作者：
Lin WC
中科院分区：
文献类型：
--
作者：
Li SC;Liao YL;Ho MR;Tsai KW;Lai CH;Lin WC
MicroRNAs （miRNAs）是一种小的非蛋白质编码rna。miRNA基因需要几个生物发生步骤才能形成功能miRNA。然而，成熟miRNA分子所涉及的确切机制和生物学尚不清楚。在本研究中，我们使用NGS平台进行了深入的分析，以检查臂选择和同分异构体。我们用Solexa平台对来自一对正常和胃肿瘤组织的小rna进行测序。通过分析NGS数据，我们量化了胃组织中mirna和isomir的表达谱。然后，我们测量了相同pre-miRNAs的5p臂和3p臂的表达比。并且，我们使用Kolmogorov-Smirnov （KS）检验来检验组织间的isomiR模式差异。我们的研究结果显示，由相同的前miRNA衍生的5p臂和3p臂miRNA具有不同的组织表达偏好，一个偏爱正常组织，另一个偏爱肿瘤组织，这强烈暗示除了已知的氢键选择规则外，可能还有其他机制控制成熟miRNA的选择。此外，通过KS试验，我们证明了一些异构体类型优先发生在正常胃组织中，而其他类型则优先发生在肿瘤胃组织中。通过使用深度测序NGS数据，人类癌症中的臂选择和异构体模式显着不同。本研究结果为miRNA调控研究提供了一个新的研究课题。随着先进的生物信息学和分子生物学研究，在不久的将来可以获得更有力的结论和对miRNA调控的深入了解。
MicroRNAs (miRNAs) are small non-protein-coding RNAs. miRNA genes need several biogenesis steps to form function miRNAs. However, the precise mechanism and biology involved in the mature miRNA molecules are not clearly investigated. In this study, we conducted in-depth analyses to examine the arm selection and isomiRs using NGS platform. We sequenced small RNAs from one pair of normal and gastric tumor tissues with Solexa platform. By analyzing the NGS data, we quantified the expression profiles of miRNAs and isomiRs in gastric tissues. Then, we measured the expression ratios of 5p arm to 3p arm of the same pre-miRNAs. And, we used Kolmogorov-Smirnov (KS) test to examine isomiR pattern difference between tissues. Our result showed the 5p arm and 3p arm miRNA derived from the same pre-miRNAs have different tissue expression preference, one preferred normal tissue and the other preferred tumor tissue, which strongly implied that there could be other mechanism controlling mature miRNA selection in addition to the known hydrogen-bonding selection rule. Furthermore, by using the KS test, we demonstrated that some isomiR types preferentially occur in normal gastric tissue but other types prefer tumor gastric tissue. Arm selections and isomiR patterns are significantly varied in human cancers by using deep sequencing NGS data. Our results provided a novel research topic in miRNA regulation study. With advanced bioinformatics and molecular biology studies, more robust conclusions and insight into miRNA regulation can be achieved in the near future.