A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)

Abstract

New types of small RNAs distinct from microRNAs (miRNAs) are progressively being discovered in various organisms. In order to discover such novel small RNAs, a library of 17-to 26-base-long RNAs was created from prostate cancer cell lines and sequenced by ultra-high-throughput sequencing. A significant number of the sequences are derived from precise processing at the 59 or 39 end of mature or precursor tRNAs to form three series of tRFs (tRNA-derived RNA fragments): the tRF-5, tRF-3, and tRF-1 series. These sequences constitute a class of short RNAs that are second most abundant to miRNAs. Northern hybridization, quantitative RT-PCR, and splinted ligation assays independently measured the levels of at least 17 tRFs. To demonstrate the biological importance of tRFs, we further investigated tRF-1001, derived from the 39 end of a Ser-TGA tRNA precursor transcript that is not retained in the mature tRNA. tRF-1001 is expressed highly in a wide range of cancer cell lines but much less in tissues, and its expression in cell lines was tightly correlated with cell proliferation. siRNAmediated knockdown of tRF-1001 impaired cell proliferation with the specific accumulation of cells in G2, phenotypes that were reversed specifically by cointroducing a synthetic 29-O-methyl tRF-1001 oligoribonucleotide resistant to the siRNA. tRF-1001 is generated in the cytoplasm by tRNA 39-endonuclease ELAC2, a prostate cancer susceptibility gene. Our data suggest that tRFs are not random by-products of tRNA degradation or biogenesis, but an abundant and novel class of short RNAs with precise sequence structure that have specific expression patterns and specific biological roles.[Keywords: Small RNA; tRNA; deep sequencing; cancer cell proliferation] Supplemental material is available at http://www.genesdev.org.

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

“…The presence of tRNA-derived RNA fragments (Lee et al 2009) has been detected also in plants Hackenberg et al 2012;Hsieh et al 2009) as well as their putative target genes (Guilherme Loss-…”

Circulating microRNA signature of genotype‐by‐age interactions in the long‐lived Ames dwarf mouse

“…Our deep sequencing studies of serum/plasma have consistently detected tRNA‐derived RNAs of size 30–33 nt (Dhahbi et al ., 2013a,b). Intracellular tRNA‐derived small RNAs are classified into two types based on their size (Sobala & Hutvagner, 2011; Martens‐Uzunova et al ., 2013): tRNA halves with size of 30–40 nt produced by cleavage of mature tRNAs, and shorter tRNA‐derived fragments (tRFs) of size 18–22 nt produced from both mature and pre‐tRNAs by Dicer or RNase Z (Thompson et al ., 2008; Cole et al ., 2009; Fu et al ., 2009; Lee et al ., 2009; Thompson & Parker, 2009a; Pederson, 2010; Sobala & Hutvagner, 2011). The tRNA halves class includes 5′‐ and 3′‐tRNA halves that were first observed in stressed cultured cells where they are produced by cleavage of tRNAs near or at the anticodon loop with the ribonuclease Rny1 in Saccharomyces cerevisiae (Thompson & Parker, 2009b) and Angiogenin in higher eukaryotes (Fu et al ., 2009; Yamasaki et al ., 2009).…”

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

“…A simple explanation is the increased coverage with ultradeep sequencing methods and coverage of any cell type including tumors, many developmental stages, as well as (tumor) cell lines numerous times over (Carninci 2009;Ritz et al 2011;Haas et al 2012;Ho et al 2012;Shah et al 2012;Eswaran et al 2013;Hu et al 2013;Schonberg et al 2013;Yoshihara et al 2013). With all this overabundance, there is a debate raging between those that claim almost any identified transcript and snippet of RNA to be functional (Mattick 2003;Lee et al 2009;Carninci 2010;Kishore et al 2010;Clark et al 2011;Bernstein et al 2012;Kapranov and St Laurent 2012;Khayrullina et al 2012;Gebetsberger and Polacek 2013;Mattick and Dinger 2013) and more conservative voices (Brosius 2005c;Huttenhofer et al 2005;Robinson 2010;van Bakel et al 2010;Graur et al 2013). The writer concurs with the argumentation for spurious and stochastic transcripts (Kowalczyk et al 2012;Jensen et al 2013;Mudge et al 2013), especially as many transcription promoters are bidirectional (Seila et al 2008;Neil et al 2009;Xu et al 2009;Wei et al 2011;Uesaka et al 2014).…”