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

Marsico, Annalisa; Huska, Matthew; Lasserre, Julia; Hu, Haiyang; Vucicevic, Dubravka; Musahl, Anne; Ørom, Ulf Andersson; Vingron, Martin

doi:10.1186/gb-2013-14-8-r84

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

MPS-Authors

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Marsico, Annalisa
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Huska, Matthew
IMPRS for Computational Biology and Scientific Computing - IMPRS-CBSC (Kirsten Kelleher), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Lasserre, Julia
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Vucicevic, Dubravka
Long non-coding RNA (Ulf Andersson Ørom), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Musahl, Anne
Long non-coding RNA (Ulf Andersson Ørom), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Ørom, Ulf Andersson
Long non-coding RNA (Ulf Andersson Ørom), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Vingron, Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Marsico.pdf
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引用

Marsico, A., Huska, M., Lasserre, J., Hu, H., Vucicevic, D., Musahl, A., Ørom, U. A., & Vingron, M. (2013). PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biology, 14(8), R84-R84. doi:10.1186/gb-2013-14-8-r84.

引用: https://hdl.handle.net/11858/00-001M-0000-0019-0B37-0

要旨

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.