ELAC1 selectively trims vault RNA 3′ ends, revealing substrate partitioning between human RNase Z paralogs

In human cells, ELAC2/RNase ZL matures nuclear and mitochondrial pre-tRNAs and releases the tRNA-like small RNAs mascRNA and menRNA from the 3′ ends of MALAT1 and NEAT1. Instead, the cytosolic short paralog ELAC1/RNase ZS repairs ANKZF1-cleaved tRNAs, with its wider substrate repertoire remaining unresolved.

Here, we investigate the role of ELAC1 in RNA metabolism using transcriptome profiling, small RNA sequencing, CLIP-seq, and biochemical reconstitution. ELAC1 is dispensable for canonical tRNA processing but it is associated with structured RNA polymerase III transcripts, prominently Y RNAs and vault RNAs (vtRNAs). Purified ELAC1 cleaved all four human vtRNAs near their 3′ ends, and catalytically inactive ELAC1 in vivo binds precursor vtRNAs carrying 3′ oligoU trailers.