BCDIN3D regulates tRNA(His) 3’ fragment processing

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.