Disease-linked mutation in RNase MRP inhibits ribosome synthesis
RMRP is a nuclear gene that encodes the RNA component of the endoribonuclease complex RNase MRP. Mutations in human RMRP cause a spectrum of disorders characterised by skeletal defects, hair anomalies and immunodeficiency. RNase MRP has an evolutionarily conserved role cleaving pre-ribosomal RNA (rRNA), and several other functions have also been proposed. However, why RMRP mutations cause disease is unknown. To look for potential novel targets of RNase MRP, RNAs interacting with protein components of the complex were mapped by the technique of cross-linking and analysis of cDNAs (CRAC). This revealed interactions near the known cleavage site in yeast pre-rRNA. The same experiment in human cells unexpectedly only detected interactions with RNA components of the complex, rather than potential targets. It has previously been shown that CRISPR-mediated disruption of RMRP in immortalised cell lines causes a pre-rRNA processing defect. Here, this result was confirmed in primary mouse T cells, which additionally showed impaired proliferation when RMRP was non-specifically mutated. To answer whether disease-causing mutations also cause this phenotype, a human cell line carrying the most common patient mutation was generated with CRISPR. This showed a growth defect accompanied by an accumulation of 41S precursor rRNA and reduced mature rRNA per cell. A similar rRNA processing phenotype was also found in CHH patient fibroblasts. Finally, the RNA-bound proteome of RMRP-mutant cells was mapped by the recently developed technique of Total RNA-bound Protein Purification (TRAPP). This confirmed that mutant cells have reduced cytosolic ribosomes relative to their mitochondrial ribosomal pool, and reduced intact RNase MRP complexes. In summary, these results support the model that mutations in RMRP cause disease by inhibiting ribosome synthesis.