Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
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DOI：
10.1101/gad.17446611
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发表时间：
2011-09-15
影响因子：
10.5
通讯作者：
Rinn, John L.
中科院分区：
文献类型：
--
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
大型基因间非编码rna （lincRNAs）正在成为多种细胞过程的关键调节因子。确定单个lincrna的功能仍然是一个挑战。RNA测序（RNA-seq）和计算方法的最新进展允许对这些转录物进行前所未有的分析。在这里，我们提出了一种综合的方法来定义bb0008000个人类lincrna的参考目录。我们的目录将先前存在的注释源与转录本结合起来，这些转录本是我们从来自24种组织和细胞类型的近40亿个RNA-seq读取数据中收集的。我们通过bbbb30属性的全景来表征每个lincRNA，包括序列，结构，转录和同源性特征。我们发现，与编码基因相比，lincRNA的表达具有显著的组织特异性，并且lincRNA通常与其邻近基因共表达，尽管在一定程度上与相邻蛋白质编码基因对相似。我们区分了具有高度进化保守性的转录本的另一个子集，但可能包括短orf，可能作为lincrna或小肽。我们完整、全面、保守的人类lincRNAs参考目录揭示了lincRNAs的整体特性，并将促进这些基因的实验研究和进一步的功能分类。
Large intergenic noncoding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-seq) and computational methods allow for an unprecedented analysis of such transcripts. Here, we present an integrative approach to define a reference catalog of >8000 human lincRNAs. Our catalog unifies previously existing annotation sources with transcripts we assembled from RNA-seq data collected from similar to 4 billion RNA-seq reads across 24 tissues and cell types. We characterize each lincRNA by a panorama of >30 properties, including sequence, structural, transcriptional, and orthology features. We found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that lincRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes. We distinguish an additional subset of transcripts that have high evolutionary conservation but may include short ORFs and may serve as either lincRNAs or small peptides. Our integrated, comprehensive, yet conservative reference catalog of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes.