Upon exposure to tension tRNAs are enzymatically cleaved yielding distinct classes

Upon exposure to tension tRNAs are enzymatically cleaved yielding distinct classes of tRNA-derived fragments (tRFs). reveal a tumor suppressive function for particular tRNA-derived fragments and explain a molecular system for their actions. This transcript displacement-based system may generalize to various other tRNA ribosomal-RNA and sno-RNA fragments. Intro Transfer RNA-derived RNA fragments (tRFs) belong to a family of short non-coding RNAs (ncRNAs) present in most organisms. These RNAs can be both constitutively generated and produced in the context of stress. Constitutive tRFs are thought to arise from ribonucleolytic processing of tRNAs by Dicer (Cole et al. 2009 and RNase Z (Lee et al. 2009 The cleavage of stress-induced tRFs also known as stress-induced fragments (tiRNAs) have been shown to happen via the action of specific ribonucleases such as Angiogenin (Fu et al. 2009 While tRNAs are probably one of the most abundant ncRNA molecules in the cell (~10% of total cellular RNA) only a small PU 02 fraction of tRNAs are cleaved to produce tRFs (Thompson and Parker 2009 Multiple classes of tRFs have been identified in various cell-types organisms and induced by numerous PU 02 conditions. These classes are defined by the position of the tRNA cleavage site that gives rise to tRFs and these classes include 5′- and 3′-tRNA halves (cleaved in the anticodon loop) 5 and 3′-tRFs (also known as 3′CCA tRF) and 3′U tRFs among others (Gebetsberger and Polacek 2013 Stress-induced tRFs have been reported to mediate a stress response PU 02 which results in stress granule assembly and inhibition of protein synthesis (Emara et al. 2010 Moreover these tRFs can effect a number of cellular functions such as cell proliferation and mediating RNA inactivation through Argonaute engagement (Gebetsberger and Polacek 2013 With this study we sought to investigate if tRFs could play a role in metastatic progression. We reasoned that tRFs could have roles in malignancy progression analogous to that of specific microRNAs (Krol et al. 2010 We also reasoned that since hypoxia is definitely a major stress experienced by cells during malignancy progression tRFs Rabbit Polyclonal to MYL7. induced under hypoxic conditions may take action to curb metastatic progression. By employing next-generation small-RNA sequencing we recognized a group PU 02 of tRFs that were up-regulated under hypoxia in breast cancer cells as well as with non-transformed mammary epithelial cells. Interestingly highly metastatic breast cancer cells did not display induction of these tRFs under hypoxia suggesting a potential part for these molecules in cancer progression. We recognized a common sequence motif present PU 02 in these hypoxia-induced fragments suggesting they may interact with a common factor. By using one of these tRFs (tRFGlu) as bait we immunoprecipitated and identified the RNA-binding protein YBX1 as a factor whose mRNA-stabilizing activity is repressed by these fragments. YBX1 is a versatile RNA-binding protein with a variety of interacting partners. It is involved in many key cellular pathways and its genetic inactivation leads to embryonic lethality (Uchiumi et al. 2006 Importantly it is highly over-expressed in multiple cancer types PU 02 (Jurchott et al. 2010 Matsumoto and Bay 2005 Wu et al. 2012 By combining molecular biochemical and computational approaches we find that tRFs bind YBX1 and displace a number of known oncogenic transcripts from YBX1 thereby antagonizing YBX1 activity. YBX1 stabilizes these oncogenic transcripts and mediates their enhanced expression. The displacement of these oncogenic transcripts by tRFs represses their stability and expression-thereby suppressing metastatic progression. RESULTS Systematic identification of tRNA-derived RNA fragments in breast cancer cells Tumor cells encounter various cellular stresses during the course of cancer progression. A critical stress is reduced access to oxygen a condition known as hypoxia (Moyer 2012 Wilson and Hay 2011 Multiple regulatory programs are co-opted by tumor cells to counteract the negative impacts of hypoxic stress (Bristow and Hill 2008 For example the stabilization and activation of the transcription factor HIF1α under hypoxia results in the activation of vascular endothelial growth factor (VEGF angiogenesis; Shen and Kaelin 2013 GLUT1 (glucose transport) and carbonic anyhydrase IX (CA9 pH regulation; Semenza 1999 Recently it was reported that tRFs are produced under hypoxia and during other stress conditions (Fu et al. 2009 Given the ability of hypoxia to significantly modulate the.