PT - JOURNAL ARTICLE AU - Sarah Choudury AU - R. Keith Slotkin AU - German Martinez TI - tRNA-derived small RNAs target transposable element transcripts AID - 10.1101/085043 DP - 2016 Jan 01 TA - bioRxiv PG - 085043 4099 - http://biorxiv.org/content/early/2016/11/02/085043.short 4100 - http://biorxiv.org/content/early/2016/11/02/085043.full AB - tRNA-derived RNA fragments (tRFs) are 18-26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are cleaved by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA. We utilized the fact that many plant small RNAs direct cleavage of their target transcripts to demonstrate that where the tRF-AGO1 complex acts to specifically target and cleave endogenous transposable element (TE) mRNAs produced from transcriptionally active TEs. The data presented here demonstrate that tRFs are bona-fide regulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.