Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis.
Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis.
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通过降解组测序数据分析跟踪 microRNA 处理信号
DOI：
10.3389/fgene.2018.00546
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发表时间：
2018
影响因子：
3.7
通讯作者：
Meng Y
中科院分区：
文献类型：
--
作者：
Yu D;Xu M;Ito H;Shao W;Ma X;Wang H;Meng Y
降解组测序（degradome-seq）被广泛用于微小RNA（miRNA）靶标上的切割位点作图。本文报道了degradome-seq数据在跟踪miRNA加工中间体中的应用价值。采用“信噪比”参数提取miRNA前体上的显著降解信号。对于分析的15个物种，许多miRNA前体的加工得到了degradome-seq数据的支持。我们发现在miRBase中注释的“高置信度”miRNAs的支持率远高于“低置信度”miRNAs。对于特定物种，具有降解组支持的加工信号的miRNA的百分比随着降解组采样多样性的增加而升高。更有趣的是，miRNA前体的组织或细胞系特异性加工模式部分促成了成熟miRNA的积累模式。在这项研究中，我们还提供了一些例子来展示degradome-seq数据在miRNA注释中的价值。基于加工信号的分布，提出了一个新的模型，即miRNA前体的茎通过“单链剪切”模式被切割，并且“环到碱基”加工比以前认为的要普遍得多。总之，我们的结果揭示了degradome-seq在跟踪miRNA加工信号方面的卓越能力。
Degradome sequencing (degradome-seq) was widely used for cleavage site mapping on the microRNA (miRNA) targets. Here, the application value of degradome-seq data in tracking the miRNA processing intermediates was reported. By adopting the parameter “signal/noise” ratio, prominent degradome signals on the miRNA precursors were extracted. For the 15 species analyzed, the processing of many miRNA precursors were supported by the degradome-seq data. We found that the supporting ratio of the “high-confidence” miRNAs annotated in miRBase was much higher than that of the “low-confidence.” For a specific species, the percentage of the miRNAs with degradome-supported processing signals was elevated by the increment of degradome sampling diversity. More interestingly, the tissue- or cell line-specific processing patterns of the miRNA precursors partially contributed to the accumulation patterns of the mature miRNAs. In this study, we also provided examples to show the value of the degradome-seq data in miRNA annotation. Based on the distribution of the processing signals, a renewed model was proposed that the stems of the miRNA precursors were diced through a “single-stranded cropping” mode, and “loop-to-base” processing was much more prevalent than previously thought. Together, our results revealed the remarkable capacity of degradome-seq in tracking miRNA processing signals.
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