Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data.
Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data.
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DOI：
10.3389/fmolb.2021.727537
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发表时间：
2021
影响因子：
5
通讯作者：
Burns K
中科院分区：
文献类型：
--
作者：
Florea L;Payer L;Antonescu C;Yang G;Burns K
Alu外显子化事件在功能上使转录组多样化，产生了可变的mRNA异构体，并约占人类基因组中可变剪接（跳跃）外显子的5%。我们开发了计算方法，并将其整合到一个名为Alubaster的软件中，用于从大规模RNA - seq数据集中检测mRNA转录本中Alu序列的整合情况。该方法可检测来自固定和多态性Alu元件的Alu序列，包括参考基因组中缺失的Alu插入序列。我们将我们的方法应用于117个GTEx人类额叶皮质样本，以构建和描述一组含Alu的mRNA。特别是，我们检测并描述了在870个固定Alu位点发生的Alu外显子化，其中237个是新发现的，以及数百个涉及多态性变体或参考基因组中不存在的罕见等位基因的Alu元件的推定事件。这些方法和注释代表了一种独特且有价值的资源，可用于了解含Alu的mRNA的特征及其组织特异性表达模式。
Alu exonization events functionally diversify the transcriptome, creating alternative mRNA isoforms and accounting for an estimated 5% of the alternatively spliced (skipped) exons in the human genome. We developed computational methods, implemented into a software called Alubaster, for detecting incorporation of Alu sequences in mRNA transcripts from large scale RNA-seq data sets. The approach detects Alu sequences derived from both fixed and polymorphic Alu elements, including Alu insertions missing from the reference genome. We applied our methods to 117 GTEx human frontal cortex samples to build and characterize a collection of Alu-containing mRNAs. In particular, we detected and characterized Alu exonizations occurring at 870 fixed Alu loci, of which 237 were novel, as well as hundreds of putative events involving Alu elements that are polymorphic variants or rare alleles not present in the reference genome. These methods and annotations represent a unique and valuable resource that can be used to understand the characteristics of Alu-containing mRNAs and their tissue-specific expression patterns.