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

Annalisa Marsico1*, Matthew R Huska1, Julia Lasserre1, Haiyang Hu2, Dubravka Vucicevic1, Anne Musahl1, Ulf Andersson Orom1 and Martin Vingron1

Author affiliations

1 Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany

2 Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, 200031 Shanghai, China

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Citation and License

Genome Biology 2013, 14:R84  doi:10.1186/gb-2013-14-8-r84

Published: 16 August 2013


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 webcite

miRNA transcriptional regulation; deepCAGE; mixture model