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

• Published in: Genome biology Vol. 14; no. 8; p. R84
• Main Authors: Marsico, Annalisa, Huska, Matthew R, Lasserre, Julia, Hu, Haiyang, Vucicevic, Dubravka, Musahl, Anne, Orom, Ulf Andersson, Vingron, Martin
• Format: Journal Article
• Language: English
• Published: England Springer-Verlag 16-08-2013; BioMed Central
• Subjects: Algorithms; Brain - growth & development; Brain - metabolism; Brain Chemistry; Databases, Genetic; Gene Expression Regulation, Developmental; genomics; Genomics - methods; Humans; Introns; Method; microRNA; MicroRNAs - chemistry; MicroRNAs - genetics; Molecular Sequence Annotation; Promoter Regions, Genetic; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 1465-6906; 1474-760X; 1465-6914; 1474-760X
• DOI: 10.1186/gb-2013-14-8-r84

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 .