BCDIN3D regulates tRNAHis 3' fragment processing

PLoS Genet. 2019 Jul 22;15(7):e1008273. doi: 10.1371/journal.pgen.1008273. eCollection 2019 Jul.


5' ends are important for determining the fate of RNA molecules. BCDIN3D is an RNA phospho-methyltransferase that methylates the 5' monophosphate of specific RNAs. In order to gain new insights into the molecular function of BCDIN3D, we performed an unbiased analysis of its interacting RNAs by Thermostable Group II Intron Reverse Transcriptase coupled to next generation sequencing (TGIRT-seq). Our analyses showed that BCDIN3D interacts with full-length phospho-methylated tRNAHis and miR-4454. Interestingly, we found that miR-4454 is not synthesized from its annotated genomic locus, which is a primer-binding site for an endogenous retrovirus, but rather by Dicer cleavage of mature tRNAHis. Sequence analysis revealed that miR-4454 is identical to the 3' end of tRNAHis. Moreover, we were able to generate this 'miRNA' in vitro through incubation of mature tRNAHis with Dicer. As found previously for several pre-miRNAs, a 5'P-tRNAHis appears to be a better substrate for Dicer cleavage than a phospho-methylated tRNAHis. Moreover, tRNAHis 3'-fragment/'miR-4454' levels increase in cells depleted for BCDIN3D. Altogether, our results show that in addition to microRNAs, BCDIN3D regulates tRNAHis 3'-fragment processing without negatively affecting tRNAHis's canonical function of aminoacylation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cell Line
  • DEAD-box RNA Helicases / genetics*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Methyltransferases / genetics*
  • MicroRNAs / genetics
  • RNA, Transfer, His / metabolism*
  • Ribonuclease III / genetics*
  • Sequence Analysis, RNA
  • Transfer RNA Aminoacylation


  • MIRN4454 microRNA, human
  • MicroRNAs
  • RNA, Transfer, His
  • BCDIN3D protein, human
  • Methyltransferases
  • DICER1 protein, human
  • Ribonuclease III
  • DEAD-box RNA Helicases