RNA editing of protein sequences: A rare event in human transcriptomes
RNA editing of protein sequences: A rare event in human transcriptomes
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DOI：
10.1261/rna.033233.112
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发表时间：
2012-09-01
期刊：
影响因子：
4.5
通讯作者：
Majewski, Jacek
中科院分区：
文献类型：
--
作者：
Kleinman, Claudia L.;Adoue, Veronique;Majewski, Jacek
RNA编辑是RNA分子转录后的重新编码，对基因表达具有广泛的潜在影响。最近几项关于人类转录组的研究报告了DNA和RNA之间的大量差异，包括无法用任何已知的哺乳动物RNA编辑机制解释的事件。然而，由于高通量测序的技术限制有时被忽视，并且测序错误与编辑位点混淆，因此对rna编辑的估计存在数量级差异。在这里，我们开发了一系列计算方法来分析这一过程在人类转录组中的程度，确定并解决大规模方法的主要错误来源。我们将检测管道应用于高水平表达ADAR1的淋巴母细胞样细胞系的深度测序数据，并表明不太可能发生非规范编辑，至少85%-98%的候选位点是测序和作图的结果。通过实现一种检测无内含子基因复制的方法，我们发现以前验证的大多数非规范位点起源于这些区域内的读错定位。另一方面，规范的A-to-G编辑在非编码的Alu序列中很普遍，在外显子和编码区很少见，验证率也有所下降。我们发现的编辑位点的基因组分布，以及在研究或生物复制中缺乏一致性，表明该过程在蛋白质序列的整体重编码中具有较小的定量影响。我们提出ADAR1蛋白的主要作用是作为防御可能对基因组有害的元素的防御系统。
RNA editing, the post-transcriptional recoding of RNA molecules, has broad potential implications for gene expression. Several recent studies of human transcriptomes reported a high number of differences between DNA and RNA, including events not explained by any known mammalian RNA-editing mechanism. However, RNA-editing estimates differ by orders of magnitude, since technical limitations of high-throughput sequencing have been sometimes overlooked and sequencing errors have been confounded with editing sites. Here, we developed a series of computational approaches to analyze the extent of this process in the human transcriptome, identifying and addressing the major sources of error of a large-scale approach. We apply the detection pipeline to deep sequencing data from lymphoblastoid cell lines expressing ADAR1 at high levels, and show that noncanonical editing is unlikely to occur, with at least 85%-98% of candidate sites being the result of sequencing and mapping artifacts. By implementing a method to detect intronless gene duplications, we show that most noncanonical sites previously validated originate in read mismapping within these regions. Canonical A-to-G editing, on the other hand, is widespread in noncoding Alu sequences and rare in exonic and coding regions, where the validation rate also dropped. The genomic distribution of editing sites we find, together with the lack of consistency across studies or biological replicates, suggest a minor quantitative impact of this process in the overall recoding of protein sequences. We propose instead a primary role of ADAR1 protein as a defense system against elements potentially damaging to the genome.