PROmiRNA: a new approach for miRNA promoter annotation based on a semi-supervised statistical model

The regulation of intragenic miRNAs by their own intronic promoters is one of the open problems of miRNA biogenesis. Here, researchers from the Max Planck Institute for Molecular Genetics, Germany describe PROmiRNA, a new approach for miRNA promoter annotation based on a semi-supervised statistical model trained on deepCAGE data and sequence features. They validate their 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 one to perform a large-scale analysis of their genomic features, as well as elucidate their contribution to tissue-specific regulation.

rna-seq

Availability – PROmiRNA can be downloaded from http://promirna.molgen.mpg.de.

  • Marsico A, Huska MR, Lasserre J, Hu H, Vucicevic D, Musahl A, Andersson Orom U, Vingron M. (2013) PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol 14(8), R84. [abstract]