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

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.

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

“…Interestingly, recent studies report that these elements may contribute to gene regulation, being cleaved by DICER RNAse to produce stable RNA products rather than being just randomly generated degradation products (Haussecker et al 2010;Cole et al 2009;Sobala and Hutvagner 2011).…”

RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage

“…Defined tRNA fragments have been identified through small RNA cloning approaches (Kawaji et al 2008;Cole et al 2009;Haussecker et al 2010), suggesting a physiological role for tRNA fragments. Interestingly, tRNA fragments can be processed to smaller RNAs by the Dicer RNase, indicating a potential interaction of tRNA-derived sequences and canonical small RNA processing pathways (Cole et al 2009).…”

“…Interestingly, tRNA fragments can be processed to smaller RNAs by the Dicer RNase, indicating a potential interaction of tRNA-derived sequences and canonical small RNA processing pathways (Cole et al 2009). Indeed, a recent study provided evidence that tRNA-derived small RNAs act to down-regulate target mRNAs, and affect different RNA silencing pathways by associating with effector core components (Haussecker et al 2010).…”

tRNA modifications: Necessary for correct tRNA‐derived fragments during the recovery from stress?

“…Stress generates increased numbers of such dsRNAs, especially in the form of ''nicked'' tRNAs and tRNA fragments. Since Dicers and Argonautes can associate with tRNA-derived sequences [24,25], it follows that specific stress conditions might favor such association. Ago-2 has been found in stress granules, which also correlated with decreased RNAi in human cells [26].…”