TRNAU1AP and PRPF39 establish integrated control over processing of most abundant human non-coding RNAs

Although abundance of the metastasis-associated long non-coding RNA MALAT1 depends on the maturation of its triple-helix-containing 3′ end via non-canonical processing, the control of this step has remained unknown. Using iterative genome-wide screening, we identified TRNAU1AP and PRPF39 that together control the 3′-end processing of MALAT1, enabling a reduction in its levels. We further show that these factors form part of a previously unrecognized RNase MRP and P control (RMPPc) pathway that, in addition to MALAT1, establishes integrated control over the processing of MEN-β, internal transcribed spacers in pre-rRNA, and 5′-leader sequences in pre-tRNA, thereby impacting fundamental processes prerequisite for translation. We demonstrate that this far-reaching impact is achieved through a single control point: inclusion of the initiating ATG-containing exon 2 in RPP14, an essential component of both RNase MRP and RNase P, thereby controlling both catalytic RNAs—MRP RNA and H1 RNA. Finally, we show that upstream of this primary control point, the RMPPc pathway forms a remarkably interlinked four-pronged feedback circuit that confers stability on post-transcriptional processing of over 90% of the total RNA content in human cells. Regulation of the 3′-end processing of lncRNA MALAT1 has remained unknown. Here, the authors identified a previously unrecognized RNase MRP and P control (RMPPc) pathway that controls posttranscriptional processing of MALAT1 and over 90% of the total RNA content in human cells.