title: MicroRNA-encoding long non-coding RNAs.
abstract: BACKGROUND
  Recent analysis of the mouse transcriptional data has revealed the existence of approximately 34,000 messenger-like non-coding RNAs (ml-ncRNAs). Whereas the functional properties of these ml-ncRNAs are beginning to be unravelled, no functional information is available for the large majority of these transcripts.
  
  
  RESULTS
  A few ml-ncRNA have been shown to have genomic loci that overlap with microRNA loci, leading us to suspect that a fraction of ml-ncRNA may encode microRNAs. We therefore developed an algorithm (PriMir) for specifically detecting potential microRNA-encoding transcripts in the entire set of 34,030 mouse full-length ml-ncRNAs. In combination with mouse-rat sequence conservation, this algorithm detected 97 (80 of them were novel) strong miRNA-encoding candidates, and for 52 of these we obtained experimental evidence for the existence of their corresponding mature microRNA by microarray and stem-loop RT-PCR. Sequence analysis of the microRNA-encoding RNAs revealed an internal motif, whose presence correlates strongly (R2 = 0.9, P-value = 2.2 x 10(-16)) with the occurrence of stem-loops with characteristics of known pre-miRNAs, indicating the presence of a larger number microRNA-encoding RNAs (from 300 up to 800) in the ml-ncRNAs population.
  
  
  CONCLUSIONS
  Our work highlights a unique group of ml-ncRNAs and offers clues to their functions.
authors.affiliation: Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, PR China. heshunmin@gmail.com
authors.forename: Shunmin
authors.initials: S
authors.lastname: He
authors.forename: Hua
authors.initials: H
authors.lastname: Su
authors.forename: Changning
authors.initials: C
authors.lastname: Liu
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Housheng
authors.initials: H
authors.lastname: He
authors.forename: Dandan
authors.initials: D
authors.lastname: He
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhao
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D005260:Female; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D011247:Pregnancy; D012326:RNA Splicing; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012984:Software
chemical_list: D035683:MicroRNAs; D022661:RNA, Untranslated