Computational Analysis, Biochemical Purification, and Detection of tRNA-Derived Small RNA Fragments

  • Simon P. Keam
  • Andrew Sobala
  • David T. Humphreys
  • Catherine M. Suter
  • Gyorgy HutvagnerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1173)


The rapidly growing list of small RNA species generated by next-generation sequencing technologies has accelerated the development of new bioinformatics tools for their detection. Small RNAs generated from tRNAs, transfer RNA-derived fragments (tRFs), represent a novel challenge in accurately identifying and distinguishing them from random degradation products of tRNAs. Here, we describe a bioinformatics approach to detect tRFs in next-generation sequencing libraries. We also present a biochemical purification protocol for enriching 5′ tRFs and separating them from miRNAs. And finally, we suggest reliable methods for detecting and quantifying tRFs.


Transfer RNA fragments tRF Deep sequencing Bioinformatics Ionic exchange chromatography Northern blotting Quantitative PCR 



This work was supported by the ARC DP 130103027. G.H. is an ARC Future Fellow.


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Simon P. Keam
    • 1
  • Andrew Sobala
    • 2
  • David T. Humphreys
    • 3
  • Catherine M. Suter
    • 3
  • Gyorgy Hutvagner
    • 1
    Email author
  1. 1.Faculty of Engineering and Information Technology, Centre of Health TechnologiesUniversity of Technology, SydneySydneyAustralia
  2. 2.Department of Infectious DiseasesKing’s College London School of MedicineLondonUK
  3. 3.Molecular, Structural and Computational Biology DivisionVictor Chang Cardiac Research InstituteDarlinghurstAustralia

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