Strikingly, we found that the current analytical methods suffer from very high false positive rates and that a significant fraction of sites in the public databases cannot be validated. In this work, we present potential solutions to these problems and provide a comprehensive and extensively validated list of A-to-I editing sites in a human cancer cell line. Our findings demonstrate that most of true A-to-I editing sites in a human cancer cell line are located in the non-coding transcripts, the so-called RNA \'dark matter\'. On the other hand, many ADAR editing events occurring in exons of human protein-coding mRNAs, including those that can recode the transcriptome, represent false positives and need to be interpreted with caution. Nonetheless, yet undiscovered authentic ADAR sites that increase the diversity of human proteome exist and warrant further identification.
Accurate identification of human ADAR sites remains a challenging problem, particularly for the sites in exons of protein-coding mRNAs. As a result, genome-wide surveys of ADAR editome must still be accompanied by extensive Sanger validation efforts. However, given the vast number of unknown human ADAR sites, there is a need for further developments of the analytical techniques, potentially those that are based on deep learning solutions, in order to provide a quick and reliable identification of the editome in any sample.
结果:引人注目的是,我们发现,目前的分析方法存在很高的假阳性率,公共数据库中很大一部分网站无法验证.在这项工作中,我们提出了这些问题的潜在解决方案,并提供了人类癌细胞系中A-to-I编辑位点的全面且广泛验证的列表。我们的发现表明,人类癌细胞系中大多数真正的A到I编辑位点都位于非编码转录本中,所谓的RNA“暗物质”。另一方面,许多ADAR编辑事件发生在人类蛋白质编码mRNA的外显子中,包括那些可以重新编码转录组的,代表假阳性,需要谨慎解释。尽管如此,尚未发现的增加人类蛋白质组多样性的真正的ADAR位点存在,需要进一步鉴定。
结论:准确识别人类ADAR位点仍然是一个具有挑战性的问题,特别是蛋白质编码mRNA的外显子中的位点。因此,对ADAR编辑组的全基因组调查仍必须伴随着广泛的Sanger验证工作。然而,鉴于大量未知的人类ADAR站点,需要进一步发展分析技术,可能是基于深度学习解决方案的,以便快速可靠地鉴定任何样品中的editome。