tRNA-derived small RNAs target transposable element transcripts

Nucleic Acids Res. 2017 May 19;45(9):5142-5152. doi: 10.1093/nar/gkx103.


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 processed 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 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.

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis Proteins / metabolism
  • Base Sequence
  • DNA Transposable Elements / genetics*
  • MicroRNAs / metabolism
  • Mutation / genetics
  • Pollen / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Plant / genetics
  • RNA, Plant / metabolism*
  • RNA, Transfer / genetics
  • RNA, Transfer / metabolism*
  • Reproducibility of Results


  • Arabidopsis Proteins
  • DNA Transposable Elements
  • MicroRNAs
  • RNA, Messenger
  • RNA, Plant
  • RNA, Transfer