Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome.
Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome.
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DOI：
10.1186/s13062-017-0183-4
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发表时间：
2017-06-08
期刊：
影响因子：
5.5
通讯作者：
Hamada M
中科院分区：
文献类型：
--
作者：
Iwakiri J;Terai G;Hamada M
长链非编码rna （lncRNAs）通过其在人类转录组中的组织特异性表达，在正常组织分化和癌症发展中发挥关键作用。最近对大分子相互作用的研究表明，组织特异性lncrna与各种与组织分化相关的mrna形成碱基配对相互作用，这表明组织特异性是控制人类lncRNA-mRNA相互作用的重要因素。在这里，我们报告了通过使用各种人体组织的RNA-seq数据对lncrna和mrna的组织特异性的研究，以及通过将lncrna和mrna的组织特异性整合到我们对人类lncRNA-RNA相互作用的综合预测中来推断的组织特异性lncRNA-mRNA相互作用的计算预测。我们预测的lncRNA- mrna相互作用通过与实验验证的lncRNA- mrna相互作用（TINCR lncRNA和mrna之间的相互作用）进行比较来评估，显示预测精度比以前没有考虑lncRNA和mrna组织特异性的预测方法有所提高。此外，我们的预测表明，TINCR lncRNA的潜在功能不仅包括表皮分化，还包括通过lncRNA- mrna相互作用促进食管发育。审稿人：本文由张伟雄博士和Bojan Zagrovic博士审稿。本文的在线版本（doi:10.1186/s13062-017-0183-4）包含补充材料，仅供授权用户使用。
Long noncoding RNAs (lncRNAs) play a key role in normal tissue differentiation and cancer development through their tissue-specific expression in the human transcriptome. Recent investigations of macromolecular interactions have shown that tissue-specific lncRNAs form base-pairing interactions with various mRNAs associated with tissue-differentiation, suggesting that tissue specificity is an important factor controlling human lncRNA-mRNA interactions. Here, we report investigations of the tissue specificities of lncRNAs and mRNAs by using RNA-seq data across various human tissues as well as computational predictions of tissue-specific lncRNA-mRNA interactions inferred by integrating the tissue specificity of lncRNAs and mRNAs into our comprehensive prediction of human lncRNA-RNA interactions. Our predicted lncRNA-mRNA interactions were evaluated by comparisons with experimentally validated lncRNA-mRNA interactions (between the TINCR lncRNA and mRNAs), showing the improvement of prediction accuracy over previous prediction methods that did not account for tissue specificities of lncRNAs and mRNAs. In addition, our predictions suggest that the potential functions of TINCR lncRNA not only for epidermal differentiation but also for esophageal development through lncRNA-mRNA interactions. Reviewers: This article was reviewed by Dr. Weixiong Zhang and Dr. Bojan Zagrovic. The online version of this article (doi:10.1186/s13062-017-0183-4) contains supplementary material, which is available to authorized users.