Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis

  1. Eugene Berezikov1,
  2. Geert van Tetering1,
  3. Mark Verheul1,
  4. Jose van de Belt1,
  5. Linda van Laake1,2,
  6. Joost Vos3,
  7. Robert Verloop3,4,
  8. Marc van de Wetering1,
  9. Victor Guryev1,
  10. Shuji Takada5,
  11. Anton Jan van Zonneveld3,
  12. Hiroyuki Mano5,
  13. Ronald Plasterk1,6, and
  14. Edwin Cuppen1
  1. 1Hubrecht Laboratory, 3584 CT Utrecht, The Netherlands;
  2. 2Department of Cardiology, HLCU Location, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands;
  3. 3Department of Nephrology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands;
  4. 4Department of Physiology, Free University Medical Center, 1081 BT Amsterdam, The Netherlands;
  5. 5Divisionof Functional Genomics, Jichi Medical School, Kawachigun, Tochigi 329-0498, Japan

Abstract

icroRNAs are 20- to 23-nucleotide RNA molecules that can regulate gene expression. Currently >400 microRNAs have been experimentally identified in mammalian genomes, whereas estimates go up to 1000 and beyond. Here we show that many more mammalian microRNAs exist. We discovered novel microRNA candidates using two approaches: testing of computationally predicted microRNAs by a modified microarray-based detection system, and cloning and sequencing of large numbers of small RNAs from different human and mouse tissues. Together these efforts experimentally identified 348 novel mouse and 81 novel human microRNA candidate genes. Most novel microRNAs candidates are not conserved beyond mammals, and ~10% are taxon-specific. Our analyses indicate that the entire microRNA repertoire is not remotely exhausted.

Footnotes

  • 6 orresponding author.

    6 -mail plasterk{at}niob.knaw.nl; fax 31-30-2516554.

  • rticle published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.5159906.

  • Supplemental material is available online at www.genome.org. All novel microRNAs described in this study are submitted to the central miRNA repository miRBase, maintained at the Wellcome Trust Sanger Institute, under the ID nos. listed in the Supplemental material.

    • Received January 20, 2006.
    • Accepted July 10, 2006.
| Table of Contents

Preprint Server