PDF(Pubmed)
Abstract：
Ribonucleotides represent the most common non-canonical nucleotides found in eukaryotic genomes. The sources of chromosome-embedded ribonucleotides and the mechanisms by which unrepaired rNMPs trigger genome instability and human pathologies are not fully understood. The available sequencing technologies only allow to indirectly deduce the genomic location of rNMPs. Oxford Nanopore Technologies (ONT) may overcome such limitation, revealing the sites of rNMPs incorporation in genomic DNA directly from raw sequencing signals. We synthesized two types of DNA molecules containing rNMPs at known or random positions and we developed data analysis pipelines for DNA-embedded ribonucleotides detection by ONT. We report that ONT can identify all four ribonucleotides incorporated in DNA by capturing rNMPs-specific alterations in nucleotide alignment features, current intensity, and dwell time. We propose that ONT may be successfully employed to directly map rNMPs in genomic DNA and we suggest a strategy to build an ad hoc basecaller to analyse native genomes.
摘要：
核糖核苷酸代表在真核基因组中发现的最常见的非规范核苷酸。染色体嵌入的核糖核苷酸的来源以及未修复的rNMP引发基因组不稳定性和人类病理的机制尚未完全了解。可用的测序技术仅允许间接推断rNMP的基因组位置。牛津纳米孔技术(ONT)可以克服这种限制，直接从原始测序信号揭示rNMP在基因组DNA中的掺入位点。我们合成了两种在已知或随机位置含有rNMP的DNA分子，并开发了用于ONT检测DNA嵌入核糖核苷酸的数据分析管道。我们报告说，ONT可以通过捕获核苷酸比对特征中的rNMPs特异性改变来识别DNA中掺入的所有四种核糖核苷酸。电流强度,和停留时间。我们建议ONT可以成功地用于直接在基因组DNA中定位rNMPs，并且我们建议一种策略来建立一个临时的碱基来分析天然基因组。
