Identifying small interfering RNA loci from high-throughput sequencing data
Identifying small interfering RNA loci from high-throughput sequencing data
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DOI：
10.1093/bioinformatics/btr687
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发表时间：
2012-02-15
期刊：
影响因子：
5.8
通讯作者：
Baulcombe, David C.
中科院分区：
文献类型：
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作者：
Hardcastle, Thomas J.;Kelly, Krystyna A.;Baulcombe, David C.
动机：小干扰RNA（siRNA）是由双链RNA前体的长得多的序列通过Dicer或Dicer样蛋白切割产生的。这些小RNA在遗传和表观遗传调控中起着关键作用;然而，充分了解它们的运作机制取决于它们所来源的前体的表征。结果：小RNA群体的高通量测序允许推断双链RNA前体的位置。我们已经开发了分析来自多个生物来源的小RNA测序数据的方法，考虑到复制信息，以鉴定稳健的siRNA前体组。我们的方法在拟南芥的一组小RNA测序数据和模拟数据集上都表现出良好的性能。
Motivation: Small interfering RNAs (siRNAs) are produced from much longer sequences of double- stranded RNA precursors through cleavage by Dicer or a Dicer-like protein. These small RNAs play a key role in genetic and epigenetic regulation; however, a full understanding of the mechanisms by which they operate depends on the characterization of the precursors from which they are derived.Results: High-throughput sequencing of small RNA populations allows the locations of the double-stranded RNA precursors to be inferred. We have developed methods to analyse small RNA sequencing data from multiple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. Our methods show good performance on both a set of small RNA sequencing data in Arabidopsis thaliana and simulated datasets.