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

Christian Cole; Andrew Sobala; Cheng Lu; Shawn R. Thatcher; Andrew Bowman; John W.S. Brown; Pamela J. Green; Geoffrey J. Barton; Gyorgy Hutvagner

doi:10.1261/rna.1738409

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

¹Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
²Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
³Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
⁴Plant Sciences Division, Scottish Crop Research Institute, University of Dundee, Invergowrie, Dundee DD2 5DA, United Kingdom
⁵Genetics Programme, Scottish Crop Research Institute, University of Dundee, Invergowrie, Dundee DD2 5DA, United Kingdom

↵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 tRNA^Gln is dependent on Dicer in vivo and that Dicer cleaves the tRNA in vitro.

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Footnotes

Reprint requests to: Gyorgy Hutvagner, Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; e-mail: g.hutvagner{at}dundee.ac.uk; fax: 44-1382-386310; or Geoffrey J. Barton, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; e-mail: g.j.barton{at}dundee.ac.uk; fax: 44-1382-385764.
Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.1738409.
- Received May 18, 2009.
- Accepted September 3, 2009.