title: Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding genes. miRNAs play a very important role in diverse biological processes and various diseases. Many algorithms are able to predict miRNA genes and their targets, but their transcription regulation is still under investigation. It is generally believed that intragenic miRNAs (located in introns or exons of protein coding genes) are co-transcribed with their host genes and most intergenic miRNAs transcribed from their own RNA polymerase II (Pol II) promoter. However, the length of the primary transcripts and promoter organization is currently unknown.
  
  
  METHODS
  We performed Pol II chromatin immunoprecipitation (ChIP)-chip using a custom array surrounding regions of known miRNA genes. To identify the true core transcription start sites of the miRNA genes we developed a new tool (CPPP). We showed that miRNA genes can be transcribed from promoters located several kilobases away and that their promoters share the same general features as those of protein coding genes. Finally, we found evidence that as many as 26% of the intragenic miRNAs may be transcribed from their own unique promoters.
  
  
  CONCLUSIONS
  miRNA promoters have similar features to those of protein coding genes, but miRNA transcript organization is more complex.
authors.affiliation: Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.
authors.forename: David L
authors.initials: DL
authors.lastname: Corcoran
authors.forename: Kusum V
authors.initials: KV
authors.lastname: Pandit
authors.forename: Ben
authors.initials: B
authors.lastname: Gordon
authors.forename: Arindam
authors.initials: A
authors.lastname: Bhattacharjee
authors.forename: Naftali
authors.initials: N
authors.lastname: Kaminski
authors.forename: Panayiotis V
authors.initials: PV
authors.lastname: Benos
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology; D018899:CpG Islands; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism*; D022661:RNA, Untranslated / Q000235:genetics
chemical_list: D035683:MicroRNAs; D022661:RNA, Untranslated; D012319:RNA Polymerase II