Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)

RNA. 2021 Apr;27(4):477-495. doi: 10.1261/rna.077701.120. Epub 2021 Jan 14.


tRNA-derived fragments (tRFs) have recently gained a lot of scientific interest due to their diverse regulatory roles in several cellular processes. However, their function in dynamic biological processes such as development and regeneration remains unexplored. Here, we show that tRFs are dynamically expressed during planarian regeneration, suggesting a possible role for these small RNAs in the regulation of regeneration. In order to characterize planarian tRFs, we first annotated 457 tRNAs in S. mediterranea combining two tRNA prediction algorithms. Annotation of tRNAs facilitated the identification of three main species of tRFs in planarians-the shorter tRF-5s and itRFs, and the abundantly expressed 5'-tsRNAs. Spatial profiling of tRFs in sequential transverse sections of planarians revealed diverse expression patterns of these small RNAs, including those that are enriched in the head and pharyngeal regions. Expression analysis of these tRF species revealed dynamic expression of these small RNAs over the course of regeneration suggesting an important role in planarian anterior and posterior regeneration. Finally, we show that 5'-tsRNA in planaria interact with all three SMEDWI proteins and an involvement of AGO1 in the processing of itRFs. In summary, our findings implicate a novel role for tRFs in planarian regeneration, highlighting their importance in regulating complex systemic processes. Our study adds to the catalog of posttranscriptional regulatory systems in planaria, providing valuable insights on the biogenesis and the function of tRFs in neoblasts and planarian regeneration.

Keywords: planaria; regeneration; small RNA; tRFs; tRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Argonaute Proteins / genetics*
  • Argonaute Proteins / metabolism
  • Base Pairing
  • Base Sequence
  • Gene Expression Regulation
  • Helminth Proteins / genetics*
  • Helminth Proteins / metabolism
  • Molecular Sequence Annotation
  • Nucleic Acid Conformation
  • Planarians / genetics*
  • Planarians / metabolism
  • RNA, Helminth / chemistry
  • RNA, Helminth / classification
  • RNA, Helminth / genetics*
  • RNA, Helminth / metabolism
  • RNA, Small Untranslated / chemistry
  • RNA, Small Untranslated / classification
  • RNA, Small Untranslated / genetics*
  • RNA, Small Untranslated / metabolism
  • RNA, Transfer / chemistry
  • RNA, Transfer / classification
  • RNA, Transfer / genetics*
  • RNA, Transfer / metabolism
  • Regeneration / genetics*


  • Argonaute Proteins
  • Helminth Proteins
  • RNA, Helminth
  • RNA, Small Untranslated
  • RNA, Transfer