长非编码RNA(Long noncoding RNAs,lncRNA)是一类新型调控分子,近期研究发现其在从胚胎发育到肿瘤发生等多种生理病理过程中发挥核心调控作用[1–5]。因此,随着越来越多的长非编码RNA被鉴定[6, 7],一批计算工具应运而生,为生物学家预测lncRNA的GO功能和调控网络[8]、亚细胞定位[9,10],乃至lncRNA-RNA[11]、lncRNA-蛋白[12]相互作用等提供了重要的工具。然而,这些工具仅支持从单一角度对长非编码RNA进行注释,难以涵盖lncRNA的功能全谱。
2016年,北京大学高歌课题组开发了长非编码RNA在线注释平台AnnoLnc[13],基于700多套高通量数据和先进的计算流程实现了对任意人类长非编码RNA 从序列结构到进化模式的全面注释。作为国际首个长非编码RNA在线注释平台,AnnoLnc自2016年11月正式上线以来已成为相关领域的主流工具,支撑了来自全球5万余用户提交的近7千万条序列分析,并获邀为SpringNature Methods in Molecular Biology系列丛书撰写专题介绍章节。
日前,高歌课题组在此基础上全面更新升级了AnnoLnc平台。新版本AnnoLnc2整合了十个注释模块(图1),注释内容涵盖了序列和结构、表达和调控、功能和相互作用、以及演化和遗传关联,为研究长非编码RNA的功能及其作用机制提供了高效、全面的分析平台,并为后续的生物学研究提供了重要的线索。例如,演化模块的注释结果可以揭示长非编码RNA是否具有保守的功能[14];亚细胞定位模块的注释结果可以揭示它们在何处发挥功能[15];功能富集模块的注释结果可以揭示它们发挥怎样的功能[16];miRNA调控和蛋白相互作用模块的注释结果可以揭示潜在的功能机制[17, 18]等。
图1. AnnoLnc2框架
图2. AnnoLnc2 网页界面。用户可通过一个三步骤的操作运行AnnoLnc2(A),并查看详细的注释结果,以及批量下载所有的注释结果(B)
为了满足批量分析的需求,AnnoLnc2还为用户提供了可进行大规模线下分析的单机版本(下载链接:http://annolnc.gao-lab.org/download.php)。该单机版不仅包含了在线版本的全部功能,还支持自定义模块和自定义注释数据,用户可以基于自产数据(如RNA-seq数据)指定感兴趣的模块进行批量分析。
AnnoLnc2网址:http://annolnc.gao-lab.org/
原文链接:https://doi.org/10.1093/nar/gkaa368
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