Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences

Mamm Genome. 2006 Oct;17(10):1033-41. doi: 10.1007/s00335-006-0007-9. Epub 2006 Oct 3.


MicroRNAs (miRNAs) are a class of approximately 22-nt small RNAs that regulate posttranscriptional gene expression. Thousands of expressed sequence tags (ESTs) have been identified by using upstream 2500-nt and downstream 4000-nt flanking sequences to BLAST in the dbEST database. The cotranscription of the miRNAs and their flanking sequences covered by the matched ESTs is verified by RT-PCR. It directly reveals that a large portion of mammalian intergenic miRNAs are first transcribed as long primary transcripts (pri-miRNAs). Also, the transcripts' ranges of tens of pri-miRNAs are predicted by the EST-extension method. We then extracted the tissue-specific expression information from the annotations of the matched ESTs and established the expression profile of the studied miRNAs for tens of tissues. This provided a new way to establish the expression profiles of miRNAs. Results show that the human brain, lung, liver, and eye and the mouse brain, eye, and mammary gland are tissues in which enriched numbers of miRNAs are expressed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Flanking Region*
  • 5' Flanking Region*
  • Animals
  • Animals, Newborn
  • Brain / metabolism
  • Chromosome Mapping / methods*
  • Computational Biology
  • DNA, Intergenic / chemistry*
  • Databases, Nucleic Acid
  • Expressed Sequence Tags*
  • Gene Expression Profiling / methods*
  • Humans
  • Kidney / metabolism
  • Mammals
  • Mice
  • MicroRNAs / metabolism*
  • Rats
  • Spleen / metabolism


  • DNA, Intergenic
  • MicroRNAs