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 semisupervised 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.
CITATION STYLE
Marsico, A., Huska, M. R., Lasserre, J., Hu, H., Vucicevic, D., Musahl, A., … Vingron, M. (2013). PROmiRNA: A new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biology, 14(8). https://doi.org/10.1186/gb-2013-14-8-r84
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