title: Computational analysis, biochemical purification, and detection of tRNA-derived small RNA fragments.
abstract: 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.
authors.affiliation: Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology, Sydney, 235 Jones Street, Ultimo, Sydney, NSW, 2007, Australia.
authors.forename: Simon P
authors.initials: SP
authors.lastname: Keam
authors.forename: Andrew
authors.initials: A
authors.lastname: Sobala
authors.forename: David T
authors.initials: DT
authors.lastname: Humphreys
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Suter
authors.forename: Gyorgy
authors.initials: G
authors.lastname: Hutvagner
mesh_terms: D001483:Base Sequence; D015152:Blotting, Northern / Q000379:methods; D002852:Chromatography, Ion Exchange / Q000379:methods; D030561:Databases, Nucleic Acid; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D020407:Internet; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D058727:RNA, Small Untranslated / Q000032:analysis / Q000235:genetics* / Q000302:isolation & purification*; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics
chemical_list: D058727:RNA, Small Untranslated; D012343:RNA, Transfer