title: PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs.
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.
authors: Annalisa
authors: A
authors: Marsico
authors: Matthew R
authors: MR
authors: Huska
authors: Julia
authors: J
authors: Lasserre
authors: Haiyang
authors: H
authors: Hu
authors: Dubravka
authors: D
authors: Vucicevic
authors: Anne
authors: A
authors: Musahl
authors: Ulf
authors: U
authors: Orom
authors: Martin
authors: M
authors: Vingron
mesh_terms: D000465:Algorithms; D001921:Brain / Q000254:growth & development / Q000378:metabolism*; D001923:Brain Chemistry; D030541:Databases, Genetic; D018507:Gene Expression Regulation, Developmental; D023281:Genomics / Q000379:methods*; D006801:Humans; D007438:Introns; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D058977:Molecular Sequence Annotation; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors
references: Bioinformatics. 2006 Jul 1;22(13):1658-9
references: 16731699
references: Genome Biol. 2009;10(4):R40
references: 19374775
references: PLoS One. 2012;7(4):e34092
references: 22523544
references: EMBO J. 2007 Feb 7;26(3):775-83
references: 17255951
references: Mol Cell. 2007 Jun 8;26(5):745-52
references: 17540599
references: Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1412-7
references: 16432200
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D105-10
references: 19906716
references: Nucleic Acids Res. 2011 Nov;39(21):9345-56
references: 21821656
references: Genome Res. 2012 Sep;22(9):1634-45
references: 22955976
references: RNA. 2004 Dec;10(12):1957-66
references: 15525708
references: Proc Natl Acad Sci U S A. 2005 Mar 8;102(10):3627-32
references: 15738415
references: Genome Res. 2009 Oct;19(10):1742-51
references: 19713549
references: Bioinformatics. 2007 Jan 15;23(2):134-41
references: 17098775
references: Nat Rev Mol Cell Biol. 2009 Feb;10(2):126-39
references: 19165215
references: Nat Rev Genet. 2011 Nov 18;12(12):846-60
references: 22094948
references: BMC Bioinformatics. 2010 Feb 18;11:94
references: 20167110
references: Genome Res. 2012 Apr;22(4):611-22
references: 22300767
references: Genes Dev. 2008 Nov 15;22(22):3172-83
references: 19056895
references: Genome Res. 2010 Sep;20(9):1207-18
references: 20647238
references: J Comput Biol. 2010 Aug;17(8):953-67
references: 20726790
references: Genome Biol. 2009;10(7):R79
references: 19624849
references: PLoS Comput Biol. 2008 Mar 21;4(3):e1000039
references: 18369429
references: Nature. 2009 Feb 19;457(7232):1028-32
references: 19169241
references: Genome Res. 1997 Sep;7(9):861-78
references: 9314492
references: Nat Rev Genet. 2010 Sep;11(9):597-610
references: 20661255
references: Nat Protoc. 2011 Nov 03;6(12):1860-9
references: 22051799
references: Mol Carcinog. 2014 Feb;53(2):117-24
references: 22930395
references: Nat Genet. 2006 Jun;38(6):626-35
references: 16645617
references: Cancer Res. 2012 Apr 15;72(8):1921-8
references: 22496456
references: Bioinformatics. 2008 Feb 1;24(3):303-8
references: 18055479
references: Genome Res. 2011 Mar;21(3):447-55
references: 21106904
references: Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17719-24
references: 17965236
references: Biotechniques. 2008 Apr;44(5):627-8, 630, 632
references: 18474037
references: Genome Res. 2009 Apr;19(4):644-56
references: 19141595
references: Nat Rev Genet. 2007 Feb;8(2):93-103
references: 17230196
references: RNA. 2010 Mar;16(3):495-505
references: 20075166
references: Cancer Cell. 2006 Jun;9(6):435-43
references: 16766263
references: Nat Protoc. 2008;3(10):1578-88
references: 18802439
references: Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15776-81
references: 14663149
references: Cell Commun Signal. 2009 Aug 10;7:18
references: 19664273
references: Cell. 2008 Aug 8;134(3):521-33
references: 18692474
references: Nat Cell Biol. 2009 Mar;11(3):228-34
references: 19255566
references: Bioinformatics. 2010 Mar 15;26(6):841-2
references: 20110278
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7
references: 21037258
references: Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12481-6
references: 16885212
references: Genomics. 2011 Jan;97(1):1-6
references: 20977933
references: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references: 15034147
references: Bioinformatics. 2006 Jul 15;22(14):e472-80
references: 16873509
references: PLoS Comput Biol. 2007 Mar 9;3(3):e37
references: 17352530
references: Brief Bioinform. 2009 Sep;10(5):498-508
references: 19531545
references: Mol Cell Biol. 2009 Jun;29(12):3243-54
references: 19349299
references: Genome Res. 2009 Feb;19(2):266-75
references: 18997002