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September 5, 2025Open Access

Composition and RNA binding specificity of metazoan RNase MRP

YLYuan LiuCM Hospital SHShiyang HeUniversity of California, Los Angeles KPKawon PyoUniversity of California, Riverside

Key Points

RMP64 and RMP24 are essential for the maturation of rRNA in mammalian cells, highlighting their critical role.
The study reveals a suite of RNA-binding targets for RNase MRP, including nucleotide-level cleavage sites.
Unique metazoan RNase MRP subunits were identified, distinguishing it from closely related RNase P complexes.
These findings underscore the importance of RNase MRP in maintaining cell proliferation through rRNA processing.

Abstract

Ribonuclease (RNase) MRP is a conserved RNA-based enzyme best known for its essential role in the maturation of ribosomal RNA (rRNA) in eukaryotes. However, the composition and RNA substrate specificity of this multisubunit ribonucleoprotein complex in higher eukaryotes remain a mystery. Here, we identify NEPRO and C18ORF21 (which we renamed RMP64 and RMP24, respectively) as constitutive subunits of metazoan RNase MRP. These proteins are unique to RNase MRP and absent from the closely related RNase P, which processes transfer RNA (tRNA) precursors and tRNA-like substrates. We find that RMP64 and RMP24 are integral subunits of RNase MRP, stabilize its catalytic RNA, and are required for rRNA maturation and cell proliferation. Leveraging these discoveries, we identify a broad suite of in vivo RNA-binding targets of each enzyme, including potential cleavage sites at nucleotide resolution. Our findings identify the first metazoan RNase MRP-specific protein subunits and define the RNA-targeting repertoire of this essential enzyme in mammalian cells.

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