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

Genome Biol. 2013 Aug 16;14(8):R84. 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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Brain / growth & development
  • Brain / metabolism*
  • Brain Chemistry
  • Databases, Genetic
  • Gene Expression Regulation, Developmental
  • Genomics / methods*
  • Humans
  • Introns
  • MicroRNAs / chemistry
  • MicroRNAs / genetics*
  • Molecular Sequence Annotation
  • Promoter Regions, Genetic*
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism


  • MicroRNAs
  • Transcription Factors