MicroRNA-encoding long non-coding RNAs

BMC Genomics. 2008 May 21:9:236. doi: 10.1186/1471-2164-9-236.


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.

Conclusion: Our work highlights a unique group of ml-ncRNAs and offers clues to their functions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Chromosome Mapping
  • Conserved Sequence
  • Databases, Nucleic Acid
  • Female
  • Male
  • Mice
  • Mice, Inbred C57BL
  • MicroRNAs / chemistry
  • MicroRNAs / genetics*
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Oligonucleotide Array Sequence Analysis
  • Pregnancy
  • RNA Splicing
  • RNA, Untranslated / chemistry
  • RNA, Untranslated / genetics*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Software


  • MicroRNAs
  • RNA, Untranslated