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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 tRNA His  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 tRNA His . Sequence analysis revealed that miR-4454 is identical to the 3’ end of tRNA His . Moreover, we were able to generate this ‘miRNA’  in vitro  through incubation of mature tRNA His  with Dicer. As found previously for several pre-miRNAs, a 5’P-tRNA His  appears to be a better substrate for Dicer cleavage than a phospho-methylated tRNA His . Moreover, tRNA His  3’-fragment/‘miR-4454’ levels increase in cells depleted for BCDIN3D. Altogether, our results show that in addition to microRNAs, BCDIN3D regulates tRNA His  3’-fragment processing without negatively affecting tRNA His ’s canonical function of aminoacylation.

BCDIN3D regulates tRNAHis 3’ fragment processing