Marsico Annalisa, Huska Matthew R, Lasserre Julia, Hu Haiyang, Vucicevic Dubravka, Musahl Anne, Orom Ulf, Vingron Martin
Genome Biol. 2013 Aug 16;14(8):R84. doi: 10.1186/gb-2013-14-8-r84.
The regulation of intragenic miRNAs by their own intronic promoters is one of the open problems of miRNA biogenesis. Here, we describe PROmiRNA, a new approach for miRNA promoter annotation based on a semi-supervised statistical model trained on deepCAGE data and sequence features. We validate our results with existing annotation, PolII occupancy data and read coverage from RNA-seq data. Compared to previous methods PROmiRNA increases the detection rate of intronic promoters by 30%, allowing us to perform a large-scale analysis of their genomic features, as well as elucidate their contribution to tissue-specific regulation. PROmiRNA can be downloaded from http://promirna.molgen.mpg.de.
基因内miRNA受其自身内含子启动子的调控是miRNA生物合成中尚未解决的问题之一。在此，我们描述了PROmiRNA，这是一种基于在deepCAGE数据和序列特征上训练的半监督统计模型进行miRNA启动子注释的新方法。我们用现有的注释、RNA聚合酶II占位数据以及RNA测序数据的读取覆盖度来验证我们的结果。与之前的方法相比，PROmiRNA将内含子启动子的检测率提高了30%，使我们能够对其基因组特征进行大规模分析，并阐明它们对组织特异性调控的作用。PROmiRNA可从http://promirna.molgen.mpg.de下载。
