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PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs

2013; BioMed Central; Volume: 14; Issue: 8 Linguagem: Inglês

10.1186/gb-2013-14-8-r84

1474-760X

Annalisa Marsico, Matthew R. Huska, Julia Lasserre, Hai Hu, Dubravka Vučićević, Anne Musahl, Ulf Andersson Ørom, Martin Vingron,

RNA Interference and Gene Delivery

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.