Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs (original) (raw)

  1. Christian Cole1,6,
  2. Andrew Sobala2,6,
  3. Cheng Lu3,
  4. Shawn R. Thatcher3,
  5. Andrew Bowman2,
  6. John W.S. Brown4,5,
  7. Pamela J. Green3,
  8. Geoffrey J. Barton1 and
  9. Gyorgy Hutvagner2
  10. 1Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
  11. 2Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
  12. 3Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
  13. 4Plant Sciences Division, Scottish Crop Research Institute, University of Dundee, Invergowrie, Dundee DD2 5DA, United Kingdom
  14. 5Genetics Programme, Scottish Crop Research Institute, University of Dundee, Invergowrie, Dundee DD2 5DA, United Kingdom
  15. ↵6 These authors contributed equally to this work.

Abstract

Deep sequencing technologies such as Illumina, SOLiD, and 454 platforms have become very powerful tools in discovering and quantifying small RNAs in diverse organisms. Sequencing small RNA fractions always identifies RNAs derived from abundant RNA species such as rRNAs, tRNAs, snRNA, and snoRNA, and they are widely considered to be random degradation products. We carried out bioinformatic analysis of deep sequenced HeLa RNA and after quality filtering, identified highly abundant small RNA fragments, derived from mature tRNAs that are likely produced by specific processing rather than from random degradation. Moreover, we showed that the processing of small RNAs derived from tRNAGln is dependent on Dicer in vivo and that Dicer cleaves the tRNA in vitro.

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