C18orf21/RMP24 and Nepro/RMP64 are RNase MRP-specific subunits required for 40S ribosome biogenesis

RNase P and RNase MRP are evolutionarily-related ribonucleoprotein complexes that share common protein subunits, but carry out distinct site-specific endonuclease activities. Here, we identify two RNase MRP-specific proteins C18orf21 (RMP24) and Nepro (RMP64). C18orf21 contains a structurally similar N-terminal domain to Rpp21, but has a distinct subcellular localization and RNA-binding specificity, allowing C18orf21 to uniquely associate with RNase MRP. We ectopically express C18orf21 (RNase MRP specific), Nepro (RNase MRP specific), Rpp21 (RNase P specific), and Rpp14 (shared subunit), with a C-terminal GFP and performed RIP-seq to identify bound RNAs. Our data provide a model to understand C18orf21 physical interactions along with its role in ribosomal RNA processing. In addition to this, we knock out C18orf21, Rpp21, and Rpp14 and analyze their transcriptome. We additionally analyze rRNA intermediates in knockout cells. Overall design: Biological replicates for RIP-seq were defined as replicate doxycycline inductions of GFP transgenes.Biological replicates for RNA-seq experiments were defined as repliate lentiviral infections/knockouts. N=2 biological replicates were performed for each experiment.