Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.
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DOI：
10.1093/nar/gkp093
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发表时间：
2009-05
影响因子：
14.9
通讯作者：
Fahlman RP
中科院分区：
文献类型：
--
作者：
Ebhardt HA;Tsang HH;Dai DC;Liu Y;Bostan B;Fahlman RP
dna测序技术的最新进展使得获得小RNA序列的大型数据集成为可能。在这里，我们证明并非所有非完全匹配的小RNA序列都是简单的技术测序错误，但许多具有有价值的生物信息。对来自水稻和拟南芥小RNA测序项目的三个小RNA数据集的分析表明，在同源非相同小RNA序列比对时，许多单核苷酸替代错误重叠。对替代错误位点和身份的研究表明，许多替代错误可能源于转录后修饰或RNA编辑。修饰包括tRNA中n1 -甲基修饰的嘌呤核苷酸，微RNA中潜在的脱氨或碱基取代，3 ‘微RNA尿嘧啶延伸和5 ’微RNA缺失。此外，对大型测序数据集的进一步分析表明，5 ‘缺失和3 ’尿苷延伸的联合作用可以改变微rna与不同Argonaute蛋白结合的特异性。因此，我们证明，并非所有小RNA数据集中的测序错误都是技术人工产物，但这些错误实际上往往揭示了转录后RNA修饰位点的有价值的生物学见解。
Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous non-identical small RNA sequences. Investigating the sites and identities of substitution errors reveal that many potentially originate as a result of post-transcriptional modifications or RNA editing. Modifications include N1-methyl modified purine nucleotides in tRNA, potential deamination or base substitutions in micro RNAs, 3′ micro RNA uridine extensions and 5′ micro RNA deletions. Additionally, further analysis of large sequencing datasets reveal that the combined effects of 5′ deletions and 3′ uridine extensions can alter the specificity by which micro RNAs associate with different Argonaute proteins. Hence, we demonstrate that not all sequencing errors in small RNA datasets are technical artifacts, but that these actually often reveal valuable biological insights to the sites of post-transcriptional RNA modifications.
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