iRNA-3typeA: Identifying Three Types of Modification at RNA's Adenosine Sites.
iRNA-3typeA: Identifying Three Types of Modification at RNA's Adenosine Sites.
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DOI：
10.1016/j.omtn.2018.03.012
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发表时间：
2018-06-01
期刊：
影响因子：
--
通讯作者：
Chou KC
中科院分区：
文献类型：
--
作者：
Chen W;Feng P;Yang H;Ding H;Lin H;Chou KC
RNA修饰是向核苷酸添加化学基团或其局部结构变化。了解这些修饰的发生位点，对于深入了解其生物学功能和机制以及治疗某些基因组疾病都是至关重要的。随着后基因组时代产生的大量RNA序列，已经提出了许多计算方法来逐一识别各种类型的RNA修饰。然而，到目前为止，还没有开发出用于同时鉴定几种不同类型的RNA修饰的方法。为了应对这一挑战，我们开发了一种名为“iRNA-3 typeA”的预测器，通过该预测器，我们可以同时识别RNA中以下三种最常见修饰的发生位点：（1）N1-甲基腺苷（m1A），（2）N6-甲基腺苷（m6 A）和（3）腺苷到肌苷（A-to-I）。通过对来自智人和小家鼠转录组的RNA序列进行严格的交叉验证，已经表明强大的新预测因子实现的成功率相当高。为了方便广大实验科学家，在http://lin-group.cn/server/iRNA-3typeA/上建立了一个用户友好的iRNA-3 typeA网络服务器。预期iRNA-3 typeA可能成为基因组分析的有用的高通量工具。
RNA modifications are additions of chemical groups to nucleotides or their local structural changes. Knowledge about the occurrence sites of these modifications is essential for in-depth understanding of the biological functions and mechanisms and for treating some genomic diseases as well. With the avalanche of RNA sequences generated in the post-genomic age, many computational methods have been proposed for identifying various types of RNA modifications one by one. However, so far no method whatsoever has been developed for simultaneously identifying several different types of RNA modifications. To address such a challenge, we developed a predictor called “iRNA-3typeA,” by which we can simultaneously identify the occurrence sites of the following three most frequently observed modifications in RNA: (1) N1-methyladenosine (m1A), (2) N6-methyladenosine (m6A), and (3) adenosine to inosine (A-to-I). It has been shown via rigorous cross-validations for the RNA sequences from Homo sapiens and Mus musculus transcriptomes that the success rates achieved by the powerful new predictor are quite high. For the convenience of broad experimental scientists, a user-friendly web server for iRNA-3typeA has been established at http://lin-group.cn/server/iRNA-3typeA/. It is anticipated that iRNA-3typeA may become a useful high throughput tool for genome analysis.
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