PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs |
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| Authors: | Annalisa Marsico Matthew R Huska Julia Lasserre Haiyang Hu Dubravka Vucicevic Anne Musahl Ulf Andersson Orom Martin Vingron |
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| Affiliation: | 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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| Abstract: | 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. |
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